Divergence in size,but not in shape: variation in skull size and shape within Ommatotriton newts

Using a geometric morphometric approach, we explored the variation in skull size and skull shape in banded newts (genus Ommatotriton). The genus Ommatotriton is represented by two allopatric, genetically well‐defined species: Ommatotriton ophryticus and O. vittatus. Within each species, two subspecies have been recognised. The samples used in this study cover the geographical and genetic variation within each species. We found statistically significant variation in skull size between species and among populations within species. When corrected for size, there was no significant variation in shape between species. Our results indicate that the variation in skull shape within the genus Ommatotriton is almost entirely due to size‐dependent, allometric shape changes. The exception is the shape of the ventral skull in males. Males of O. ophryticus and O. vittatus significantly diverge in the shape of the ventral cranium. The ventral skull, more precisely the upper jaw and palate, is directly functionally related to feeding. In general, our results indicate that allometry is a significant factor in the morphological variation of banded newts. However, the divergence in the ventral skull shape of males indicates that sexual selection and niche partitioning may have influenced the evolution of skull shape in these newts.     

ALLOZYME DIVERSITY WITHIN AND DIVERGENCE AMONG FOUR SPECIES OF ROBINSONIA (ASTERACEAE: SENECIONEAE), A GENUS ENDEMIC TO THE JUAN FERNANDEZ ISLANDS,CHILE

Enzyme electrophoresis was employed to assess genetic diversity within and divergence among four species of Robinsonia (R. evenia, R. gayana, R. gracilis, R. thurifera), a genus endemic to the Juan Fernandez Islands, Chile. The genus consists of treelike perennial plants, and all species are dioecious. Morphological diversity within the genus is reflected by recognition of two subgenera, with three sections in one subgenus. Total gene diversity is highest in the two species (R. gayana and R. gracilis) that are most common and have the largest population sizes. Robinsonia evenia has only half and the rare R. thurifera only 20% of the diversity detected in the other two species. The diversity measured in R. gayana and R. gracilis is comparable to the values typical of continental species of flowering plants with similar life history attributes. The genetic identities between species range from 0.560 to 0.706, which is similar to or below many values for congeneric species, but much lower than most reports for congeners on oceanic islands. The higher diversity within and divergence among species of Robinsonia compared to many insular endemics may result from several factors. The genus probably arose from selfincompatible plants of the genus Senecio, which means that several to perhaps many colonizers carried considerable allozymic variation to the Islands. Large population sizes and obligate outcrossing are additional factors that would account for higher diversity. Sorting of alleles during radiation and the process of mutation probably combined to produce divergence among the species. Estimated divergence times calculated for the species from allozyme data range from 1.7 to 5.5 million years depending on the assumptions made in the calculations; the age of the island (Masatierra) on which these four species are confined is approximately 4.0 million years. The electrophoretic data suggest that Robinsonia arrived early in the archipelago, and radiated and speciated rapidly after colonization.     

Geographic variation and divergence of songs in the Olive Sparrow species complex

Phenotypic traits such as songs are important in species recognition. Variation in acoustic traits can form barriers to gene flow and promote speciation. Therefore, understanding song divergence is crucial in groups with controversial taxonomy such as Olive Sparrows (Arremonops rufivirgatus), a widespread Neotropical species of songbird with multiple allopatric populations. Taxonomic authorities disagree on the number of Olive Sparrow subspecies, placing them into either two or three main groups. These groups may represent separate species based on morphological traits, but trait divergence within the complex has not been examined. We studied geographic variation in the characteristics of the songs of Olive Sparrows at two geographical levels: among three proposed groups and among five allopatric populations. In a second analysis, we evaluated the strength of acoustic divergence within the complex by comparing acoustic distances among groups and allopatric populations of Olive Sparrows with the acoustic distance among three recognized species in the genus Arremonops. We analyzed 802 songs from 174 individuals across 81 locations and measured 12 variables to describe the fine structural characteristics of the songs of Olive Sparrows, Green-backed Sparrows (A. chloronotus), Black-striped Sparrows (A. conirostris), and Tocuyo Sparrows (A. tocuyensis). We found significant acoustic variation in the Olive Sparrow complex at both geographical levels. Our divergence analysis also revealed that vocal divergence within the complex is similar to or greater than that found between recognized species in the genus. Together, these results suggest that acoustic diversity within the Olive Sparrow complex probably originated by isolation in tandem with selective and/or non-selective factors.     

Mitochondrial phylogeography of a leafminer parasitoid, Diglyphus isaea (Hymenoptera: Eulophidae) in China

Diglyphus isaea is one of the primary parasitoids of agromyzid leafminers. Mitochondrial cytochrome oxidase subunit I sequences from 10 Chinese localities were used to investigate geographic variation within this widespread and morphologically uniform parasitoid. Phylogeographic analyses and sequence variation indicated that this species was actually a species-complex. We used an amber fossil record of the genus Entedon (Eulophidae: Entedoninae) as a reference to estimate the divergence time of major clades within D. isaea. With reference to the fossil record of its hosts, our results indicate that associations between parasitoids and leaf-miners could have been possibly established 38.2 million years ago.     

Diversification and biogeographic history of the Western Palearctic freshwater flatworm genus Schmidtea (Tricladida: Dugesiidae), with a redescription of Schmidtea nova

The freshwater flatworm genus Schmidtea is endemic in the Western Palearctic region, where it is represented by only four species, thus contrasting with the high species diversity of the closely related genus Dugesia within Europe. Although containing an important model species in developmental and regeneration research, viz. Schmidtea mediterranea, no evolutionary studies on the genus Schmidtea have been undertaken. For the first time, we present a well‐resolved molecular phylogenetic tree of the four species of the genus, inferred on the basis of two molecular markers, and provide also the first detailed morphological account of Schmidtea nova. The phylogenetic tree generated corroborates an earlier speciation hypothesis based on karyological data and points to chromosomal rearrangements as the main drivers of speciation in this genus. The high genetic divergence between the four species, in combination with previous dating studies and their current geographic distribution, suggests that Schmidtea could have originated in Laurasia but lost most of its diversity during the Oligocene. Thus, its present distribution pattern may be the result of the expansion of three of its four relictual species over Europe, probably after the Pleistocene glaciations. Our detailed morphological study of S. nova revealed that it shows a number of remarkable features: interconnected testis follicles, parovaria, an ejaculatory duct exiting into the primary as well as the secondary seminal vesicle by means of a nipple, and the wall of the distal section of the ejaculatory duct being sclerotic or chitinized.     

Petrocephalus of Odzala offer insights into evolutionary patterns of signal diversification in the Mormyridae, a family of weakly electrogenic fishes from Africa

Electric signals of mormyrid fishes have recently been described from several regions of Africa. Members of the Mormyridae produce weak electric organ discharges (EODs) as part of a specialized electrosensory communication and orientation system. Sympatric species often express distinctive EODs, which may contribute to species recognition during mate choice in some lineages. Striking examples of interspecific EOD variation within assemblages have been reported for two monophyletic radiations: the Paramormyrops of Gabon and the Campylomormyrus of Lower Congo. Here, we describe a speciose assemblage of Petrocephalus in the Lékoli River system of Odzala National Park, Republic of Congo. This widespread genus comprises the subfamily (Petrocephalinae) that is the sister group to all other mormyrids (Mormyrinae). Eleven Petrocephalus species were collected in Odzala, five of which are not described taxonomically. We quantify EOD variation within this assemblage and show that all eleven species produce EOD waveforms of brief duration (species means range from 144 to 663 μs) compared to many other mormyrids. We also present reconstructed phylogenetic relationships among species based on cytochrome b sequences. Discovery of the Odzala assemblage greatly increases the number of Petrocephalus species for which EODs and DNA sequence data are available, permitting a first qualitative comparison between mormyrid subfamilies of the divergence patterns that have been described within lineages. We find that the Petrocephalus assemblage in Odzala is not a monophyletic radiation. Genetic divergence among Petrocephalus species often appears higher than among Paramormyrops or Campylomormyrus species. In contrast, results of this study and others suggest that Petrocephalus may generally exhibit less interspecific EOD divergence, as well as smaller sex differences in EOD waveforms, compared to Paramormyrops and Campylomormyrus. We discuss possible causes and consequences of EOD diversification patterns observed within mormyrid subfamilies as a framework for future comparative studies of signal evolution using this emerging model system.     

Chromosomes,DNA sequences,and evolution in salamanders of the genus Aneides

Chromosomes and DNA sequence homologies have been studied in salamanders of the genus Aneides. The species studied included A. ferreus, flavipunctatus, lugubris, hardii and aeneus. All species have 14 chromosomes. The karyotypes of A. ferreus and A. hardii are very similar. All chromosomes are metacentric or sub-metacentric except chromosome 13 which is telocentric in A. hardii, but is represented by a telocentric and a sub-telocentric chromosome in A. ferreus. C values range from 35.2 to 46.0 pg. Salamanders from different species groups have nothing in common with respect to that fraction of their repeated DNA sequences that hybridizes in experiments involving the binding of labelled whole complementary RNA from one species to whole DNA from another species. Salamanders from the same species group (ferreus, lugubris and flavipunctatus) have about 25% in common with respect to their repetitive DNA sequences.     

Species formation and geographical range evolution in a genus of Central American cloud forest salamanders (Dendrotriton)

Aim Montane Central America offers an ideal system for testing geographical hypotheses of species diversification. We examined how the complex geological history of Nuclear Central America has shaped the diversification of a genus of cloud‐forest‐inhabiting salamanders (Dendrotriton). We applied parametric models of geographical range evolution to determine the predominant mode of species formation within the genus and to test existing hypotheses of geographical species formation in the region. Location Montane cloud forests of Nuclear Central America. Methods We estimated a species tree for Dendrotriton using a multi‐locus DNA sequence data set and several coalescent methods, and performed molecular dating for divergence events within the genus. We then applied the species‐tree estimate to a likelihood‐based time‐stratified model of geographical range evolution, based on current species distributions and available geological information for Central America. Results Species trees from all methods contain two groups, one corresponding to species from the Sierra de los Cuchumatanes and the other containing all remaining species. In most cases, species formation within the genus involved an even division of the geographical range of the ancestral species between descendant species. The ancestor of extant Dendrotriton species was estimated to have occurred in either the Sierra de los Cuchumatanes or the Sierra Madre de Chiapas, and both of these areas appear to have been important for diversification within the genus. The single species found in the Quaternary‐age Guatemalan volcanic cordillera dispersed to the volcanoes from an older highland area. Main conclusions Models of geographical range evolution, when combined with robust species‐tree estimates, provide insight into the historical biogeography of taxa not available from phylogenies or distributional data alone. Vicariant species formation, rather than peripatric or gradient speciation, appears to have been the dominant process of diversification, with most divergence events occurring within or between ancient highland areas. The apparent dispersal of Dendrotriton to the Quaternary‐age volcanoes raises the possibility that the rich salamander community there is composed of species that dispersed from geologically older areas. The Motagua Valley appears not to have been as important in vicariant species formation within Dendrotriton as it is within other groups.     

Chloroplast DNA-based phylogeny of AsianPinus species (Pinaceae)

The genusPinus includes over 90 species with approximately 24 species native to Asia. We have analyzed the chloroplast (cp) DNA variation of 18Pinus species, including 15 Asian, two Eurasian, and one European species using seven restriction enzymes and ten non-overlapping probes and inferred their phylogenetic relationships. Results of phenetic and cladistic approaches to phylogeny reconstruction were largely in agreement, suggesting two major lineages within the genus and confirmed the ancient character of haploxylon and diploxylon subgenera. Species from sectionParrya appear to have diverged earliest from the hypothesized phylogenetic centre for the haploxylon pines, withP. bungeana andP. gerardiana forming two basal, monotypic lineages. The range of estimated pairwise nucleotide substitutions per site ( ) was higher among haploxylon pines than among diploxylon species. CpDNA divergence was found to be low within the sectionSylvestres, relative to the divergence among haploxylon species, suggesting that the radiation of this group of taxa from its common ancestor occurred after the diversification of other groups. The low cpDNA divergence in this subsection corroborated earlier evidence for its phylogenetic cohesiveness and existence as a monophyletic group.     

PHYLOGENY OF CHLAMYDOMONAS (CHLOROPHYTA) BASED ON CLADISTIC ANALYSIS OF NUCLEAR 18S rRNA SEQUENCE DATA1

The genus Chlamydomonas Ehrenberg may contain as many as 450 described species. Morphological, physiological and molecular data show that variation among some Chlamydomonas species can he great, leading to speculation that multiple, generic-level lineages exist within this genus. The most recent systematic studies of Chlamydomonas have led to proposals of nine distinct morphological and 15 distinct sporangial autolysin groups. Partial sequences from the nuclear small subunit rRNAs from 14 Chlamydomonas species representing 12 autolysin and four morphological groups, and from three flagellates thought to he related to Chlamydomonas were determined in a phylogenetic study of relationships among these algae. Sequence comparisons among some Chlamydomonas species revealed differences comparable to the sequence divergence between soybeans and cycads. Cladistic analysis of the sequence data suggests that multiple lineages exist among species of Chlamydomonas. Some of these lineages represent alliances of both Chlamydomonas and non-Chlamydomonas taxa; thus, the current taxonomy does not reflect natural, or monophyletic, groups. Collectively, these lineages may represent distinct families or even orders.     

Species boundaries in Malagasy snakes of the genus Madagascarophis (Serpentes: Colubridae sensu lato) assessed by nuclear and mitochondrial markers

We studied mitochondrial divergence in 27 individuals of colubrid snakes of the genus Madagascarophis Mertens from most of its distribution area in Madagascar. Combined analyses of 16S rRNA and cytochrome b sequences identified six major clades which only partly agreed with previously proposed classifications. Analysis of nuclear DNA sequences of the c-mos gene as well as of ISSR fingerprints revealed consistent differences only among three clades which we consider as distinct species: a widespread Madagascarophis colubrinus (Schlegel), with M. citrinus (Boettger) as a junior synonym, a southern M. meridionalis Domergue, and a presumably undescribed species from the extreme north of Madagascar. The species M. ocellatus Domergue was not available for our study. Within M. colubrinus there are two populations from the north-west, each showing two divergent haplotypes with pairwise divergences of up to 5.2% in the cytochrome b gene. Maximum divergence in this gene within M. colubrinus was 7.1%. These high values emphasise that caution needs to be applied before genetic distance values are used for species delimitation. Phylogeographically, most of the genetic variation in M. colubrinus is found in northern Madagascar, indicating that the species might have originated in this region. Later one haplotype clade colonised western and eastern Madagascar, with a putative secondary introgression into north-western populations.     

Characteristics of nuclear DNA in the genus Oryza

Summary DNAs have been isolated from various Oryza species and studied using physical techniques. The percent of guanine plus cytosine has been determined by thermal denaturation. While the base composition varied between the species, no heterogeneity in the base pair distribution was observed. Renaturation kinetics data of DNAs from different species show that the proportion of repeated DNA sequences vary considerably depending on the DNA content per cell, whereas the nonrepetitive DNA component remains relatively constant. These results suggest that in addition to a small range of DNA variation between the species, changes in the base composition and proportion of repeated sequences have accompanied divergence of the species within the genus.     

High mitochondrial diversity in geographically widespread butterflies of Madagascar: A test of the DNA barcoding approach

The standardized use of mitochondrial cytochrome c oxidase subunit I (COI) gene sequences as DNA barcodes has been widely promoted as a high-throughput method for species identification and discovery. Species delimitation has been based on the following criteria: (1) monophyletic association and less frequently (2) a minimum 10× greater divergence between than within species. Divergence estimates, however, can be inflated if sister species pairs are not included and the geographic extent of variation within any given taxon is not sampled comprehensively. This paper addresses both potential biases in DNA divergence estimation by sampling range-wide variation in several morphologically distinct, endemic butterfly species in the genus Heteropsis, some of which are sister taxa. We also explored the extent to which mitochondrial DNA from the barcode region can be used to assess the effects of historical rainforest fragmentation by comparing genetic variation across Heteropsis populations with an unrelated forest-associated taxon Saribia tepahi. Unexpectedly, generalized primers led to the inadvertent amplification of the endosymbiont Wolbachia, undermining the use of universal primers and necessitating the design of genus-specific COI primers alongside a Wolbachia-specific PCR assay. Regardless of the high intra-specific genetic variation observed, most species satisfy DNA barcoding criteria and can be differentiated in the nuclear phylogeny. Nevertheless, two morphologically distinguishable candidate species fail to satisfy the barcoding 10× genetic distance criterion, underlining the difficulties of applying a standard distance threshold to species delimitation. Phylogeographic analysis of COI data suggests that forest fragmentation may have played an important role in the recent evolutionary diversification of these butterflies. Further work on other Malagasy taxa using both mitochondrial and nuclear data will provide better insight into the role of historical habitat fragmentation in species diversification and may potentially contribute to the identification of priority areas for conservation.     

Adaptive radiation in miniature: the minute salamanders of the Mexican highlands (Amphibia: Plethodontidae: Thorius)

The small size and apparent external morphological similarity of the minute salamanders of the genus Thorius have long hindered evolutionary studies of the group. We estimate gene and species trees within the genus using mitochondrial and nuclear DNA from nearly all named and many candidate species and find three main clades. We use this phylogenetic hypothesis to examine patterns of morphological evolution and species coexistence across central and southern Mexico and to test alternative hypotheses of lineage divergence with and without ecomorphological divergence. Sympatric species differ in body size more than expected after accounting for phylogenetic relationship, and morphological traits show no significant phylogenetic signal. Sympatric species tend to differ in a combination of body size, presence or absence of maxillary teeth, and relative limb or tail length, even when they are close relatives. Sister species of Thorius tend to occupy climatically similar environments, which suggests that divergence across climatic gradients does not drive species formation in the genus. Rather than being an example of cryptic species formation, Thorius more closely resembles an adaptive radiation, with ecomorphological divergence that is bounded by organism‐level constraints. © 2013 The Linnean Society of London, Biological Journal of the Linnean Society, 2013, 109 , 622–643.     

Variability of 18S rDNA locus among Symphysodon fishes: chromosomal rearrangements

Three species of cichlids belonging to the genus Symphysodon have demonstrated interspecific and intraspecific variation in nucleolus organizer regions (NOR) detected with silver nitrate. In order to understand the evolution of this marker in the genus, the structural variability of these sequences in mitotic chromosomes from Symphysodon aequifasciatus, Symphysodon discus and Symphysodon haraldi was investigated using both silver nitrate impregnation and hybridization of the 18S rRNA gene probe. For the three species, the two markers were intraspecifically and interspecifically variable both in the number and in the size of the sites. This polymorphism may stem from duplications and translocations, which suggests that structural chromosome rearrangements effectively act in the karyoevolution of wild Symphysodon species and may have favoured the adaptability of these fishes to diverse aquatic environments in the Amazon.     

Selection and demographic history shape the molecular evolution of the gamete compatibility protein bindin in Pisaster sea stars

Reproductive compatibility proteins have been shown to evolve rapidly under positive selection leading to reproductive isolation, despite the potential homogenizing effects of gene flow. This process has been implicated in both primary divergence among conspecific populations and reinforcement during secondary contact; however, these two selective regimes can be difficult to discriminate from each other. Here, we describe the gene that encodes the gamete compatibility protein bindin for three sea star species in the genus Pisaster. First, we compare the full‐length bindin‐coding sequence among all three species and analyze the evolutionary relationships between the repetitive domains of the variable second bindin exon. The comparison suggests that concerted evolution of repetitive domains has an effect on bindin divergence among species and bindin variation within species. Second, we characterize population variation in the second bindin exon of two species: We show that positive selection acts on bindin variation in Pisaster ochraceus but not in Pisaster brevispinus, which is consistent with higher polyspermy risk in P. ochraceus. Third, we show that there is no significant genetic differentiation among populations and no apparent effect of sympatry with congeners that would suggest selection based on reinforcement. Fourth, we combine bindin and cytochrome c oxidase 1 data in isolation‐with‐migration models to estimate gene flow parameter values and explore the historical demographic context of our positive selection results. Our findings suggest that positive selection on bindin divergence among P. ochraceus alleles can be accounted for in part by relatively recent northward population expansions that may be coupled with the potential homogenizing effects of concerted evolution.     

Chromosome evolution and phylogeny in Ronderosia (Orthoptera,Acrididae, Melanoplinae): clues of survivors to the challenge of sympatry?

In an attempt to unveil the origin of neo‐sex chromosomes in Ronderosia Cigliano grasshoppers, we performed a combined phylogenetic analysis based on morphological (external morphology and male genitalia) and molecular data (COI, COII, 16S and ITS2) to explore the chromosome evolution within the genus. We also analysed the distributional patterns of the various Ronderosia species and considered the possible role of chromosome rearrangements (CRs) in speciation processes within the genus in the light of ‘suppressed‐recombination’ models. We mapped the states of three chromosomal characters on the combined tree topology. The combined evidence supported Ronderosia as a monophyletic group. The cytogenetic analyses of the genus demonstrated the importance of rearranged karyotypes with single, complex and multiples neo‐sex chromosome determination systems in all species. The chromosome character optimisation suggests X‐autosome centric fusion as the mechanism responsible for neo‐sex chromosome formation in most Ronderosia species, except in R. dubia and R. bergii. Similar autosomes were involved in fusions with the ancestral X chromosome in Ronderosia, supporting previous hypotheses on the unique origin of X‐autosome fusion for the sex chromosome in the genus. As a source of chromosome variation, autosome‐autosome centric fusion played a secondary role in Ronderosia compared with other Dichroplini. Given the homogeneity in the morphological features, the sympatric distribution of closely related species and the intrinsic property of centric fusion as suppressors of the crossing over, we suggest that CRs may have played a key role during the speciation process within Ronderosia.