Colonization, population expansion, and lineage turnover: phylogeography of Mesoamerican characiform fish

We present a phylogeographical analysis of four genera of Mesoamerican primary freshwater fish ( Brycon , Bryconamericus , Eretmobrycon , and Cyphocharax ). Three hundred and thirty-nine individuals were genotyped into one of 31 operational taxonomic units (OTUs) based on the nucleotide sequence of their mitochondrial ATPase 6 & 8 genes (842–839 bp). Contrary to inference based on the species-level taxonomy of these genera, molecular data identified only a single case of sympatry between closely related OTUs, despite extensive parapatry. Polytomies dominate the mtDNA-based phylogenies and demonstrate multiple, noncontemporaneous waves of rapid expansion across Mesoamerica from South American sources. Analyses based on genetic distances observed among congeneric species of Mesoamerican primary freshwater fishes in comparison to divergence between transisthmian marine fishes permit the strong inference that the Pliocene rise of the Panama land bridge provided the first opportunity for the colonization of Mesoamerica by Characiform fishes. We develop a priority-effect model, based on the assumption that genetically closely related OTUs share similar ecological niches, to reconcile the general lack of contemporary sympatry between closely related OTUs with the substantial historical connectivity among Mesoamerican drainages demonstrated by the rapid expansion of Brycon , Bryconamericus , and Cyphocharax . Finally, in most cases, we infer that the westerly limits of freshwater fish distributions in Mesoamerica are more consistent with being defined by ecological factors rather than by dispersal limitation.  © 2006 The Linnean Society of London, Biological Journal of the Linnean Society , 2006, 88 , 235–255.     

Seed dormancy in relation to seed storage behaviour in Acer

Dormancy in seeds of Acer opalus is shown to be mainly caused by the seed coats, although a slight embryo dormancy exists in fresh seeds. The ability to germinate after drying indicates that seed storage behaviour is orthodox. Recalcitrant seeds were heavier than orthodox seeds not only within section Acer but also within the whole genus after statistical control of phylogeny, through a phylogenetic ANOVA with data from two different Acer phylogenies. An evolutionary change from orthodox to recalcitrant behaviour is postulated for genus Acer , but this change appears not to have been accompanied by a change in seed dormancy, at least in the taxonomic section in which Acer opalus belongs.  © 2004 The Linnean Society of London, Botanical Journal of the Linnean Society , 2004, 145 , 203–208.     

Evolution of “determinants” in sex-determination: A novel hypothesis for the origin of environmental contingencies in avian sex-bias

Sex-determination is commonly categorized as either “genetic” or “environmental”—a classification that obscures the origin of this dichotomy and the evolution of sex-determining factors. The current focus on static outcomes of sex-determination provides little insight into the dynamic developmental processes by which some mechanisms acquire the role of sex determinants. Systems that combine “genetic” pathways of sex-determination (i.e., sex chromosomes) with “environmental” pathways (e.g., epigenetically induced segregation distortion) provide an opportunity to examine the evolutionary relationships between the two classes of processes and, ultimately, illuminate the evolution of sex-determining systems. Taxa with sex chromosomes typically undergo an evolutionary reduction in size of one of the sex chromosomes due to suppressed recombination, resulting in pronounced dimorphism of the sex chromosomes, and setting the stage for emergence of epigenetic compensatory mechanisms regulating meiotic segregation of heteromorphic sex chromosomes. Here we propose that these dispersed and redundant regulatory mechanisms enable environmental contingency in genetic sex-determination in birds and account for frequently documented context-dependence in avian sex-determination. We examine the evolution of directionality in such sex-determination as a result of exposure of epigenetic regulators of meiosis to natural selection and identify a central role of hormones in integrating female reproductive homeostasis, resource allocation to oocytes, and offspring sex. This approach clarifies the evolutionary relationship between sex-specific molecular genetic mechanisms of sex-determination and non-sex-specific epigenetic regulators of meiosis and demonstrates that both can determine sex. Our perspective shows how non-sex-specific mechanisms can acquire sex-determining function and, by establishing the explicit link between physiological integration of oogenesis and sex-determination, opens new avenues to the studies of adaptive sex-bias and sex-specific resource allocation in species with genetic sex-determination.     

Correlated evolution of sex and reproductive mode in corals (Anthozoa: Scleractinia)

Sexuality and reproductive mode are two fundamental life-history traits that exhibit largely unexplained macroevolutionary patterns among the major groups of multicellular organisms. For example, the cnidarian class Anthozoa (corals and anemones) is mainly comprised of gonochoric (separate sex) brooders or spawners, while one order, Scleractinia (skeleton-forming corals), appears to be mostly hermaphroditic spawners. Here, using the most complete phylogeny of scleractinians, we reconstruct how evolutionary transitions between sexual systems (gonochorism versus hermaphrodism) and reproductive modes (brooding versus spawning) have generated large-scale taxonomic patterns in these characters. Hermaphrodites have independently evolved in three large, distantly related lineages consisting of mostly reef-building species. Reproductive mode in corals has evolved at twice the rate of sexuality, while the evolution of sexuality has been heavily biased: gonochorism is over 100 times more likely to be lost than gained, and can only be acquired by brooders. This circuitous evolutionary pathway accounts for the prevalence of hermaphroditic spawners among reef-forming scleractinians, despite their ancient gonochoric heritage.     

The impact of endosymbionts on the evolution of host sex-determination mechanisms

The past years have revealed that inherited bacterial endosymbionts are important sources of evolutionary novelty for their eukaryotic hosts. In this review we discuss a fundamental biological process of eukaryotes influenced by bacterial endosymbionts: the mechanisms of sex determination. Because they are maternally inherited, several endosymbionts of arthropods, known as reproductive parasites, have developed strategies to convert non-transmitting male hosts into transmitting females through feminization of genetic males and parthenogenesis induction. Recent investigations have also highlighted that endosymbionts can impact upon host sex determination more subtly through genetic conflicts, resulting in selection of host nuclear genes resisting endosymbiont effects. Paradoxically, it is because of their selfish nature that reproductive parasites are such powerful agents of evolutionary change in their host sex-determination mechanisms. They might therefore represent excellent models for studying transitions between sex-determining systems and, more generally, the evolution of sex-determination mechanisms in eukaryotes.     

On the temporal inconsistencies of Linnean taxonomic ranks

The inconsistency problem in systematics refers in part to the fact that disparate taxa of identical Linnean rank are not necessarily similar or even readily comparable in any other specifiable biological feature. This shortcoming led to a ‘temporal banding’ proposal in which extant clades associated with particular taxonomic ranks would be standardized according to a universal metric: the absolute time of evolutionary origin. However, one underexplored possibility is that same‐level taxa in disparate organismal groups already might be similar (fortuitously so) in evolutionary age. In the present study, we explicitly address this possibility by reviewing published molecular inferences about the known or suspected origination dates of taxonomic genera, families, and orders in diverse organismal groups. Our findings empirically confirm that currently recognized taxa are far from temporally standardized, thereby adding support for the contention that this kind of taxonomic inconsistency should ultimately be rectified in our biological classifications. © 2011 The Linnean Society of London, Biological Journal of the Linnean Society, 2011, 102 , 707–714.     

Evolution of micromorphological and chemical characters in the lichen-forming fungal family Pertusariaceae

Micromorphological characters of the fruiting bodies, such as ascus-type and hymenial amyloidity, and secondary chemistry have been widely employed as key characters in Ascomycota classification. However, the evolution of these characters has yet not been studied using molecular phylogenies. We have used a combined Bayesian and maximum likelihood based approach to trace character evolution on a tree inferred from a combined analysis of nuclear and mitochondrial ribosomal DNA sequences. The maximum likelihood aspect overcomes simplifications inherent in maximum parsimony methods, whereas the Markov chain Monte Carlo aspect renders results independent of any particular phylogenetic tree. The results indicate that the evolution of the two chemical characters is quite different, being stable once developed for the medullary lecanoric acid, whereas the cortical chlorinated xanthones appear to have been lost several times. The current ascus-types and the amyloidity of the hymenial gel in Pertusariaceae appear to have been developed within the family. The basal ascus-type of pertusarialean fungi remains unknown.  © 2006 The Linnean Society of London, Biological Journal of the Linnean Society , 2006, 89 , 615–626.     

The phylogenetic significance of colour patterns in marine teleost larvae

Ichthyologists, natural‐history artists, and tropical‐fish aquarists have described, illustrated, or photographed colour patterns in adult marine fishes for centuries, but colour patterns in marine fish larvae have largely been neglected. Yet the pelagic larval stages of many marine fishes exhibit subtle to striking, ephemeral patterns of chromatophores that warrant investigation into their potential taxonomic and phylogenetic significance. Colour patterns in larvae of over 200 species of marine teleosts, primarily from the western Caribbean, were examined from digital colour photographs, and their potential utility in elucidating evolutionary relationships at various taxonomic levels was assessed. Larvae of relatively few basal marine teleosts exhibit erythrophores, xanthophores, or iridophores (i.e. nonmelanistic chromatophores), but one or more of those types of chromatophores are visible in larvae of many basal marine neoteleosts and nearly all marine percomorphs. Whether or not the presence of nonmelanistic chromatophores in pelagic marine larvae diagnoses any major teleost taxonomic group cannot be determined based on the preliminary survey conducted, but there is a trend toward increased colour from elopomorphs to percomorphs. Within percomorphs, patterns of nonmelanistic chromatophores may help resolve or contribute evidence to existing hypotheses of relationships at multiple levels of classification. Mugilid and some beloniform larvae share a unique ontogenetic transformation of colour pattern that lends support to the hypothesis of a close relationship between them. Larvae of some tetraodontiforms and lophiiforms are strikingly similar in having the trunk enclosed in an inflated sac covered with xanthophores, a character that may help resolve the relationships of these enigmatic taxa. Colour patterns in percomorph larvae also appear to diagnose certain groups at the interfamilial, familial, intergeneric, and generic levels. Slight differences in generic colour patterns, including whether the pattern comprises xanthophores or erythrophores, often distinguish species. The homology, ontogeny, and possible functional significance of colour patterns in larvae are discussed. Considerably more investigation of larval colour patterns in marine teleosts is needed to assess fully their value in phylogenetic reconstruction. © 2013 The Authors. Zoological Journal of the Linnean Society published by John Wiley & Sons Ltd on behalf of The Linnean Society of London     

Multiple origins of viviparity,or reversal from viviparity to oviparity? The European common lizard (Zootoca vivipara,Lacertidae) and the evolution of parity

The evolution of viviparity in squamates has been the focus of much scientific attention in previous years. In particular, the possibility of the transition from viviparity back to oviparity has been the subject of a vigorous debate. Some studies have suggested this reversal is more frequent than previously thought. However, none of them provide conclusive evidence. We investigated this problem by studying the phylogenetic relationships between oviparous and viviparous lineages of the reproductively bimodal lizard species Zootoca vivipara . Our results show that viviparous populations are not monophyletic, and that several evolutionary transitions in parity mode have occurred. The most parsimonious scenario involves a single origin of viviparity followed by a reversal back to oviparity. This is the first study with a strongly supported phylogenetic framework supporting a transition from viviparity to oviparity.  © 2006 The Linnean Society of London, Biological Journal of the Linnean Society , 2006, 87 , 1–11.     

Phyllanthus section Choretropsis (Euphorbiaceae) in Brazil

Section Choretropsis genus Phyllanthus (Euphorbiaceae) is formed by plants whose branches are modified into phylloclades. Despite the suitable characteristics of phylloclades within the Phyllanthus genus, the systematics of these species are poorly understood. Morphological data are presented here to allow future revision of this taxonomic group. The section is represented by nine species distributed in South America, eight of them endemic to Brazil. Our taxonomic studies distinguish the species and propose the synonymization of nine varieties of P. klotzschianus and two varieties of P. flagelliformis based on vegetative and reproductive characters. The diversity of branching and the morphology of phylloclades are discussed.  © 2006 The Linnean Society of London, Botanical Journal of the Linnean Society , 2006, 150 , 131–164.     

An inquiline fig wasp using seeds as a resource for small male production: a potential first step for the evolution of new feeding habits?

The processes allowing evolutionary transitions in resources used by parasitic wasps are largely unknown. Microhymenopteran communities associated with figs could provide a model system to investigate such transitions. We investigate here a species of genus Idarnes . The larvae generally develop as inquilines of the pollinating wasp larvae. However, in figs where the parasitic pressure is high, eggs are laid in developing seeds. These eggs turn into small males. This is the first report of seed consumption by a fig wasp. Using an alternative resource to produce small males could provide a pathway to select for increased ability to use this resource and hence provide an intermediate step for evolving the capacity to use new resources.  © 2007 The Linnean Society of London, Biological Journal of the Linnean Society , 2007, 92 , 9–17.     

A new dwarf Coffea (Rubiaceae) from southern Cameroon

A distinctive new species of dwarf monocaulous Coffea (Rubiaceae) from Cameroon is described and illustrated. Coffea mapiana is the second dwarf monocaulous known from Cameroon. Its diagnostic characters are elucidated and its taxonomic affinities are discussed; a conservation assessment is provided.  © 2006 The Linnean Society of London, Botanical Journal of the Linnean Society , 2006, 151 , 425–430.     

Co‐evolution of the premaxilla and jaw protrusion in cichlid fishes (Heroine: Cichlidae)

The ability of Perciform fishes to protrude their jaw has likely been critical to the trophic diversification of this group, which includes approximately 20% of all vertebrates. The length of the ascending process of the premaxilla is thought to influence the maximum extent that cichlids and other Perciforms protrude their oral jaw. Using a combination of morphometrics, kinematics, and new phylogenetic hypotheses for 20 Heroine cichlid species, we tested the evolutionary relationship between the length of the premaxillary ascending process and maximum jaw protrusion. In this clade, the length of the ascending process of the premaxilla ranged from 11.6–32.7% with respect to standard length whereas maximum jaw protrusion ranged from 3.5–23.4% with respect to standard length. The evolutionary relationships among the Heroine cichlids obtained from the genetic partitions cytochrome b, S7, and RAG1 showed limited concordance. However, correlations between the length of the ascending process and maximum jaw protrusion were highly significant when examined as independent contrasts using all three topologies. Evolutionary change in the length of the ascending process of the premaxilla is likely critical for determining the amount of jaw protrusion in Perciform groups such as cichlid fishes. © 2010 The Linnean Society of London, Biological Journal of the Linnean Society, 2010, 100 , 619–629.     

Molecular phylogeny of the genus Mus (Rodentia: Murinae) based on mitochondrial and nuclear data

The genus Mus encompasses at least 38 species divided into four subgenera: Mus , Pyromys , Nannomys and Coelomys . The subgenus Mus , which comprises the house mouse and related species, is by far the most extensively studied, although the subgenus Nannomys is the most speciose. Although the relationships within the subgenus Mus are rather well characterized, those between subgenera are still unclear. In the present study, phylogenetic analyses of the whole genus were performed using a larger species sample of Nannomys than in previous studies, and a nuclear gene (IRBP) in addition to mitochondrial data (cytochrome b and 12S rRNA). Members of the Acomyinae and Murinae were used as outgroups. Separate and combined analyses were performed with maximum parsimony, maximum likelihood and Bayesian methods, and divergence times were estimated. The results showed that the monophyly of the genus Mus and of each subgenus was strongly supported by the three genes and the combined analysis. The phylogenies derived from the three genes were on the whole congruent; however, several conflicting topologies were observed such as the relationships between the three Asian species of the subgenus Mus ( caroli , cervicolor and cookii ). Increasing the taxonomic sampling of Nannomys did not satisfactorily improve the resolution of relationships between the four subgenera. In addition, molecular calibrations indicate that the Mus and Nannomys radiation coincided with major environmental changes.  © 2005 The Linnean Society of London, Biological Journal of the Linnean Society , 2005, 84 , 417–427.     

Canarian land snail diversity: conflict between anatomical and molecular data on the phylogenetic placement of five new species of Napaeus (Gastropoda, Pulmonata, Enidae)

Five new species of land snail (family Enidae) are described from La Gomera (Canary Islands) of which the majority, on the basis of anatomy alone, could be incorporated within a new supraspecific taxon. In addition to the morphological study of these new species, a region of the 16S mitochondrial gene is sequenced from three of the new species and a range of species of Napaeus from within its two subgenera ( Napaeinus and Napaeus ) . There is a disparity between the morphological and preliminary molecular phylogenetic data. Possible explanations for this conflict are discussed, as well as the evolutionary relationships among these different taxa, and it is suggested that this group may be an excellent model for further studies of adaptation and diversification.  © 2006 The Linnean Society of London, Biological Journal of the Linnean Society , 2006, 89 , 169–187.     

Sex chromosome polymorphisms in Arctic charr and their evolutionary origins

Current data on the Y-specific sex-determining region of salmonid fishes from genera Salvelinus, Salmo, and Oncorhynchus indicate variable polymorphisms in the homologous chromosomal locations of the sex-specific determining region. In the majority of the Atlantic lineage Arctic charr, including populations from the Fraser River, in Labrador Canada, as well as Swedish and Norwegian strains, the sex-determining locus maps to linkage group AC-4. Previously, sex-linked polymorphisms (i.e., variation in the associated sex-linked markers on AC-4) have been described in Arctic charr. Here, we report further evidence for intraspecific sex linkage group polymorphisms in Arctic charr (i.e., the detection of the SEX locus on either the AC-1 or AC-21 linkage group) and a possible conservation of a sex linkage arrangement in Icelandic Arctic charr and Atlantic salmon, involving sex-linked markers on the AC-1/21 homeologs and the European AS-1/6 homeologous linkage groups in Atlantic salmon. The evolutionary origins for the multiple sex-determining regions within the salmonid family are discussed. We also relate the variable sex-determining regions in salmonids to their ancestral proto-teleost karyotypic origins and compare these findings with what has been observed in other teleost species in general.     

Revealing the mechanisms of the rostral shift of pelvic fins among teleost fishes

In teleost fishes, the position of the pelvic fins shift during evolution; this positional shift seems to have diversified their locomotion and feeding behavior, thereby expanding the habitats of these fishes. Thus, such a positional shift of the pelvic fins is one of the significant features of teleost fishes from evolutionary, embryological, and taxonomic viewpoints, but no studies to date have investigated the mechanism for the rostral shift of the pelvic fins from the anal region in teleosts. Examining the fate of the prospective pelvic fin cells of the zebrafish Danio rerio and the Nile tilapia Oreochromis niloticus embryos demonstrates that the prospective pelvic fin cells are originally located near the anus, as seen in tetrapods, but their position shifts with respect to the body trunk after its protrusion from the yolk surface. In this article, we highlight such recent findings and discuss the mechanisms of pelvic fin evolution among teleost fishes.     

Polyploidy in fishes: patterns and processes

Fishes are the most speciose group of vertebrates, with more than 24 000 species. They are characterized by great diversity in ecology, morphology, life history, behaviour and physiology. Here, the phylogenetic patterns of orders in which polyploidy has been recorded are considered, with special reference to patterns of species richness and hybridization: these orders include such phylogenetically diverse taxa as the Lepidosireniformes (lungfish) and the Perciformes (perch). Examples, predominantly drawn from the Cyprinidae and Salmonidae, are used to illustrate attributes of polyploidy in fishes. It is concluded (i) that polyploidy may have been of considerable importance in the evolution of fishes, and (ii) that fishes, with their diverse life histories, represent a useful model system with which to test theories relating to the origin and consequences of polyploidy that have been derived from work on plants.  © 2004 The Linnean Society of London, Biological Journal of the Linnean Society , 2004, 82 , 431–442.     

The adductor mandibulae muscle complex in lower teleostean fishes (Osteichthyes: Actinopterygii): comparative anatomy,synonymy, and phylogenetic implications

Bony fishes of the morphologically diverse infraclass Teleostei include more than 31 000 species, encompassing almost one‐half of all extant vertebrates. A remarkable anatomical complex in teleosts is the adductor mandibulae, the primary muscle in mouth closure and whose subdivisions vary in number and complexity. Difficulties in recognizing homologies amongst adductor mandibulae subdivisions across the Teleostei have hampered the understanding of the evolution of this system and consequently its application in phylogenetic analyses. The adductor mandibulae in representatives of all lower teleost orders is described, illustrated, and compared based on broad taxonomic sampling complemented by extensive literature information. Muscle division homologies are clarified via the application of a standardized homology‐driven anatomical terminology with synonymies provided to the myological terminologies of previous studies. Phylogenetic implications of the observed variations in the adductor mandibulae are discussed and new possible synapomorphies are proposed for the Notacanthiformes, Ostariophysi, Cypriniformes, Siluriphysi, Gymnotiformes, and Alepocephaloidei. New characters corroborate the putative monophyly of the clades Albuliformes plus Notacanthiformes (Elopomorpha), Argentinoidei plus Esocoidei plus Salmonoidei (Protacanthopterygii) and Hemiodontidae plus Parodontidae (Characiformes). We further confirm the validity of characters from the adductor mandibulae previously proposed to support the monophyly of the Esocoidei and the gonorynchiform clade Gonorynchoidei plus Knerioidei. © 2014 The Linnean Society of London