A multi-locus plastid phylogenetic analysis of the pantropical genus Diospyros (Ebenaceae), with an emphasis on the radiation and biogeographic origins of the New Caledonian endemic species

We aimed to clarify phylogenetic relationships within the pantropical genus Diospyros (Ebenaceae sensu lato), and ascertain biogeographical patterns in the New Caledonian endemic species. We used DNA sequences from eight plastid regions (rbcL, atpB, matK, ndhF, trnK intron, trnL intron, trnL-trnF spacer, and trnS-trnG spacer) and included 149 accessions representing 119 Diospyros species in our analysis. Results from this study confirmed the monophyly of Diospyros with good support and provided a clearer picture of the relationships within the genus than in previous studies. Evidence from phylogenetic analyses suggests that Diospyros colonized New Caledonia multiple times. The four lineages of Diospyros in New Caledonia also differ in their degree of diversification. The molecular data indicate that one lineage is paleoendemic and derived from an ancient Australian species. The other three lineages are more closely related to several Southeast Asian species; two of them are neoendemics, and one has radiated rapidly and recently.     

Phylogeny of the tribe Colletieae (Rhamnaceae) – a sensitivity analysis of the plastid region trnL-trnF combined with morphology

The phylogenetic relationships within the tribe Colletieae (Rhamnaceae) were examined combining data from a previous morphological analysis with data from the trnL intron and trnL-F spacer. Previous studies have failed to confirm monophyly of the genus Discaria, the only genus of the tribe with an amphiantarctic distribution. The data set was analyzed using direct optimization as implemented in the computer program POY. Direct optimization searches for multiple optimal sequence alignments and is therefore well suited for analyzing DNA sequences including ambiguous alignable regions as found in the present study. Eight different costs were used for treating the indel information. Indels were treated as single events, equal to a fifth character state, or strings of gaps were treated as single events using different costs for opening a gap and extending the gap. The optimal cost set was selected by use of both character-based and topological congruence measures. Both congruence measures agreed upon a single optimal cost set. The resulting tree generally agrees with the current taxonomic treatment of the tribe Colletieae that recognizes six genera out of which three are monotypic. However, monophyly of Discaria was not supported and the results strongly suggest segregating D. nana and D. trinervis, and re-establishing the genus Ochetophila.We are grateful to the curator of the Herbario Gaspar Xuárez, Universidad de Buenos Aires (BAA), and to the curators of the Botanic Garden of the University of Copenhagen, Botanischer Garten und Botanisches Museum Berlin-Dahlem, Jardín Botánico Lucien Hauman (Facultad de Agronomía de la Universidad de Buenos Aires), Rancho Santa Ana Botanic Garden, and Royal Botanic Gardens, Melbourne, for permission to use material from their collections. María Elena Arce, María Martha Bianchi, Eugenia Chaia, and Neville Walsh kindly provided freshly collected material. We also thank Pablo A. Goloboff, Niels Klazenga, Pauline Y. Ladiges, Martín Ramírez, Ole Seberg, Llywela Williams, and two anonymous reviewers for critically reading earlier drafts of this paper. This work was supported in part by grants TG 028 (Universidad de Buenos Aires) and PIP 4027/96 (CONICET) to D. Medan. The University of Copenhagen supported Lone Aagesen (Ph.D. grant). Jürgen Kellermann received a Ph.D.-scholarship from the University of Melbourne.     

Evolution of the Chloroplast trnL-trnF Region in the Gymnosperm Lineages Taxaceae and Cephalotaxaceae

The trnL-trnF region is located in the large single-copy region of the chloroplast genome. It consists of the trnL gene, a group I intron, and the trnL-F intergenic spacer. We analyzed the evolution of the region in three gymnosperm families, Taxaceae, Cephalotaxaceae, and Podocarpaceae, with especially dense sampling in Taxaceae and Cephalotaxaceae, for which we sequenced 43 accessions, representing all species. The trnL intron has a conserved secondary structure and contains elements that are homologous across land plants, and the spacer is highly variable in length and composition. The spatial distribution of nucleotide diversity along the trnL-F region suggests that different portions of this region have different evolutionary patterns. Tandem repeats that form stem–loop structures were detected in both the trnL intron and the trnL-F spacer, and the spacer sequences contain promoter elements for the trnF gene. The presence of promoters and stem–loop structures in the trnL-F spacer and high sequence variation in this region suggest that trnL and trnF are independently transcribed. Stem–loop regions P6, P8, and P9 of the trnL intron and the trnL-F spacer (except the promoter elements) might undergo neutral evolution with respect to their escape from functional constraints.     

Phylogenetic analysis and differentiation of Veronica subgenus Stenocarpon in the Balkan Peninsula

The Balkan Peninsula is considered the most important refugium for species during the Pleistocene glaciations and today harbours c. 2000 endemic species, but we know surprisingly little about the evolution of taxa in this region. Veronica saturejoides, V. thessalica and V. erinoides are a group of closely related alpine taxa endemic to the Balkan Peninsula. Here, we analyse four DNA regions [the nuclear chalcone synthase intron (CHSi) and ribosomal internal transcribed spacer (ITS) region and the plastid rpoB‐trnC spacer and trnL‐trnL‐trnF region] and amplified fragment length polymorphism (AFLP) fingerprints to provide a phylogenetic hypothesis for the relationships among these taxa. Additionally, we analyse leaf morphological characters used to distinguish the three subspecies of V. saturejoides. The analyses support the distinction of the three subspecies based on previously intuitively suggested characters. Nuclear chalcone synthase intron data indicate that the southern taxa are genetically much more diverse than the more northern V. saturejoides subsp. saturejoides. Phylogenetic relationships inferred from this region and AFLP fingerprints support the monophyly of V. saturejoides. In contrast, plastid DNA regions suggest a closer relationship of V. saturejoides subsp. saturejoides to V. thessalica. The most likely scenario involves introgression into V. saturejoides subsp. saturejoides from V. thessalica. © 2009 The Linnean Society of London, Botanical Journal of the Linnean Society, 2009, 159 , 616–636.     

The Chloroplast trnT–trnF Region in the Seed Plant Lineage Gnetales

The trnT–trnF region is located in the large single-copy region of the chloroplast genome. It consists of the trnL intron, a group I intron, and the trnT–trnL and trnL–trnF intergenic spacers. We analyzed the evolution of the region in the three genera of the gymnosperm lineage Gnetales (Gnetum, Welwitschia, and Ephedra), with especially dense sampling in Gnetum for which we sequenced 41 accessions, representing most of the 25–35 species. The trnL intron has a conserved secondary structure and contains elements that are homologous across land plants, while the spacers are so variable in length and composition that homology cannot be found even among the three genera. Palindromic sequences that form hairpin structures were detected in the trnL–trnF spacer, but neither spacer contained promoter elements for the tRNA genes. The absence of promoters, presence of hairpin structures in the trnL–trnF spacer, and high sequence variation in both spacers together suggest that trnT and trnF are independently transcribed. Our model for the expression and processing of the genes tRNA^Thr(UGU), tRNA^Leu(UAA), and tRNA^Phe (GAA) therefore attributes the seemingly neutral evolution of the two spacers to their escape from functional constraints. [Reviewing Editor: Debashish Bhattacharya]     

Phylogenetic relationships of the genus Cheilosia and the tribe Rhingiini (Diptera, Syrphidae) based on morphological and molecular characters

The phylogenetic relationships of the tribe Rhingiini and the genus Cheilosia (Diptera, Syrphidae) were investigated using morphological and molecular characters. The genus Cheilosia is one of the most diverse lineages of hoverflies (Syrphidae). The mitochondrial protein coding gene cytochrome c oxidase subunit I (COI), and the D2‐3 region of the nuclear 28S rRNA gene were chosen for sequencing, and morphological characters were scored for both adults and immature stages. The combined dataset included 56 ingroup taxa. The datasets were analyzed separately and in conjunction, using both static and dynamic alignment under the parsimony criterion. The aim of the study was to assess the phylogenetic relationships of the tribe Rhingiini, and to explore if the subgenera of Cheilosia were supported as monophyletic clades. Results showed that the monophyly of subtribes of Rhingiini remained ambiguous, especially due to unstable phylogenetic placements of the genera Portevinia and Rhingia. We recovered most subgenera of Cheilosia as monophyletic clades. Dynamic alignment, using the optimization alignment program POY, always recovered more parsimonious topologies under all parameter weighting schemes, than did parsimony analyses using static alignment and analyzed with NONA.     

Phylogeny and biogeography of the lamioid genus <Emphasis Type="Italic">Phlomis</Emphasis> (Lamiaceae)

The genus Phlomis is one of the largest genera of subfamily Lamioideae (Lamiaceae) with more than 100 recognised species distributed in Asia, southern Europe and northern Africa. Morphological studies have suggested that the species can be split into two morphologically distinct groups that have previously been recognised as either sections or separate genera. The current study represents the first molecular phylogenetic study of the genus in which taxa representative of the entire genus are included. In contrast to considerable morphological and ecological variation among taxa, sequence variation in the trnL intron, the trnL – F intergenic spacer, and the rps16 intron was low, resulting in sparse phylogenetic resolution, particularly among the South West Asian and Mediterranean taxa. However, the results support a split of the genus into two separate groups that are recognised here as the genera Phlomoides and Phlomis in order to decrease taxonomic complexity. The close relationship between Phlomis s.l. and Eremostachys, pointed out by several authors, is confirmed, and in a noteworthy new finding, the small Asian genus Notochaete, is more closely related to the Phlomis s.l. lineage than previously assumed. The two monotypic genera Pseuderemostachys and Lamiophlomis as well as Notochaete hamosa are transferred to Phlomoides and three new combinations are made. Character optimisation analyses based on geographic distributions of all taxa show that the groups obtained by molecular phylogenetic analysis correlate well with biogeography. The results suggest that the Phlomis s.l. lineage has a Central Asian origin in an area around Western China.     

Molecular evolution of the trnL(UAA) intron in bryophytes

Structure, variability, and molecular evolution of the trnL(UAA) intron in bryophytes (mosses and liverworts) is analyzed based on more than 1000 sequences representing all classes, including comparisons of lengths and GC-contents, sequence similarities, evolutionary rates and ti/tv ratios of the major lineages and selected genera. Secondary structure analyses of the more variable stem-loop regions facilitated recognition of sequence repeats and minute inversions that often occurred independently in non-related lineages, thus supporting alignment construction and homology assessment. The most length-variable stem-loop region P8 does not share a common evolutionary history across all major bryophyte lineages. Independent nucleotide additions such as internally repeated sequence segments resulted in non-homologous P8 sequences that cannot be folded into a common P8 secondary structure, neither for all bryophytes nor for liverworts or mosses. To address evolutionary patterns, separate analyses of P6/P8 and the remaining intron (core) have to be performed, as overall values of the complete intron are misleading. It is argued that a transition bias observed above the genus level in the core structure is caused by structural constraints, not by its higher GC-content in comparison to the more AT-rich P6 and P8. Compensating base pair changes detected in highly conserved elements are often characteristic of the major bryophyte lineages (classes). Sequence divergence and evolutionary rates are generally higher in liverworts than in mosses, resulting in ambiguous alignments of P6 and P8 even within classes. In mosses, trends towards length reduction of P8 and lower evolutionary rates of the intron are observed. Average intraspecific variation is less than 1%, corresponding to 2-3 mutations in the complete intron.     

Molecular Evolution and Phylogenetic Utility of the Chloroplastrpl16Intron inChusqueaand the Bambusoideae (Poaceae)

Phylogenetic relationships withinChusquea,a diverse genus of neotropical woody bamboos, and among selected members of the Bambusoideae were explored usingrpl16intron sequence data from the chloroplast genome. Mechanisms of mutation, including slipped-strand mispairing, secondary structure, minute inversions, and base substitutions, were examined within therpl16intron, and their effects on sequence alignment and phylogenetic analysis were investigated. Thirty-five bamboo sequences were generated and two separate matrices were analyzed using maximum parsimony. In the first, 23 sequences fromChusquea,1 ofNeurolepis,and 3 outgroups were included.Neurolepiswas supported as sister toChusquea, Chusqueawas strongly supported as a monophyletic lineage, and three species ofChusqueasubg.Rettbergiawere resolved as the most basal clade within the genus. In the second analysis, 15 sequences, 14 from across the subfamily and 1 outgroup, were included. A Bambusoideae clade was recovered with the Olyreae/Parianeae (herbaceous bamboos) and the Bambuseae (woody bamboos) each supported as monophyletic. Two clades corresponding to temperate and tropical woody bamboos were derived within the Bambuseae and the tropical taxa were further split into New World and Old World clades. Therpl16intron in bamboos was found to be susceptible to frequent length mutations of multiple origins, nonindependent character evolution, and regions of high mutability, all of which created difficulties in alignment and phylogenetic analysis; nonetheless therpl16intron is phylogenetically informative at the inter- and intrageneric levels in bamboos.     

Presence of sporangia of Frankia in the rhizosphere of Discaria (Rhamnaceae)

Discaria trinervis and Discaria americana are native actinorhizal plants in Argentina. Discaria seedlings growing in N-free liquid culture, inoculated with dry soils, developed Frankia colonies in the rhizosphere. The occurrence of hyphae, vesicles and sporangia characteristic of Frankia are described in these colonies. The presence of sporangia of Frankia has previously neither been reported in the genus Discaria, nor in the other genera of the tribe Colletieae inside root nodules or outside roots. The infective capacity of the colonies has been demonstrated.     

Molecular phylogenetics of the lizard genus Microlophus (squamata:tropiduridae): aligning and retrieving indel signal from nuclear introns

We use a multigene data set (the mitochondrial locus and nine nuclear gene regions) to test phylogenetic relationships in the South American "lava lizards" (genus Microlophus) and describe a strategy for aligning noncoding sequences that accounts for differences in tempo and class of mutational events. We focus on seven nuclear introns that vary in size and frequency of multibase length mutations (i.e., indels) and present a manual alignment strategy that incorporates insertions and deletions (indels) for each intron. Our method is based on mechanistic explanations of intron evolution that does not require a guide tree. We also use a progressive alignment algorithm (Probabilistic Alignment Kit; PRANK) and distinguishes insertions from deletions and avoids the "gapcost" conundrum. We describe an approach to selecting a guide tree purged of ambiguously aligned regions and use this to refine PRANK performance. We show that although manual alignment is successful in finding repeat motifs and the most obvious indels, some regions can only be subjectively aligned, and there are limits to the size and complexity of a data matrix for which this approach can be taken. PRANK alignments identified more parsimony-informative indels while simultaneously increasing nucleotide identity in conserved sequence blocks flanking the indel regions. When comparing manual and PRANK with two widely used methods (CLUSTAL, MUSCLE) for the alignment of the most length-variable intron, only PRANK recovered a tree congruent at deeper nodes with the combined data tree inferred from all nuclear gene regions. We take this concordance as an objective function of alignment quality and present a strongly supported phylogenetic hypothesis for Microlophus relationships. From this hypothesis we show that (1) a coded indel data partition derived from the PRANK alignment contributed significantly to nodal support and (2) the indel data set permitted detection of significant conflict between mitochondrial and nuclear data partitions, which we hypothesize arose from secondary contact of distantly related taxa, followed by hybridization and mtDNA introgression.     

Phylogenetic relationships in Southern African chloridoid grasses (Poaceae) based on nuclear and chloroplast sequence data

Phylogenetic relationships in southern African members of chloridoid grasses were investigated using DNA sequences from the chloroplast trnL (UAA) 5’ exon‐ trnF (GAA) region and the nuclear ribosomal internal transcribed spacer regions. The two datasets were analysed separately before being combined into a matrix of 50 specimens, representing 38 species. The congruence between the individual data sets was assessed in a conditional combination approach and the congruent data sets were then combined into a single data set. In this analysis, the chloridoid grasses were monophyletic and two large groups, corresponding to the tribes Eragrostideae and Cynodonteae, were polyphyletic; Eragrostis, the largest genus in the subfamily, was polyphyletic. Otherwise, high support levels were found at species and generic level.     

Phylogenetics of early branching eudicots:Comparing phylogenetic signal across plastid introns,spacers,and genes

<正>Recent phylogenetic analyses revealed a grade with Ranunculales,Sabiales,Proteales,Trochodendrales, and Buxales as first branching eudicots,with the respective positions of Proteales and Sabiales still lacking statistical confidence.As previous analyses of conserved plastid genes remain inconclusive,we aimed to use and evaluate a representative set of plastid introns(group I:trnL;group II:petD,rpll6,trnK) and intergenic spacers(trnL-F,petB-petD, atpB-rbcL,rps3-rpl16) in comparison to the rapidly evolving matK and slowly evolving atpB and rbcL genes. Overall patterns of micro structural mutations converged across genomic regions,underscoring the existence of a general mutational pattern throughout the plastid genome.Phylogenetic signal differed strongly between functionally and structurally different genomic regions and was highest in matK,followed by spacers,then group II and group I introns.The more conserved atpB and rbcL coding regions showed distinctly lower phylogenetic information content.Parsimony,maximum likelihood,and Bayesian phylogenetic analyses based on the combined dataset of non-coding and rapidly evolving regions(14 000 aligned characters) converged to a backbone topology of eudicots with Ranunculales branching first,a Proteales-Sabiales clade second,followed by Trochodendrales and Buxales. Gunnerales generally appeared as sister to all remaining core eudicots with maximum support.Our results show that a small number of intron and spacer sequences allow similar insights into phylogenetic relationships of eudicots compared to datasets of many combined genes.The non-coding proportion of the plastid genome thus can be considered an important information source for plastid phylogenomics.     

Molecular phylogeny of Cypripedium (Orchidaceae: Cypripedioideae) inferred from multiple nuclear and chloroplast regions

A molecular analysis was performed on 56 taxa in the orchid genus Cypripedium using nrDNA ITS and five chloroplast regions (trnH-psbA, atpI-atpH, trnS-trnfM, trnL-F spacer, and the trnL intron). The genus Cypripedium was confirmed as monophyletic. Our data provided strong support for monophyletic grouping of eight infrageneric sections (Subtropica, Obtusipetala, Trigonopedia, Sinopedilum, Bifolia, Flabelinervia, Arietinum, and Cypripedium) defined in earlier taxonomic treatments, and paraphyletic grouping of two sections (Irapeana and Retinervi). Within the genus Cypripedium, the first divergent lineage consisted of two Mesomaerican species, and subsequently the Cypripedium debile lineage from eastern Asia was split. Our study did not support the notion that two Asian species (Cypripedium subtropicum and Cypripedium singchii) were closely related to either Mesoamerican Cypripedium irapeanum or North American Cypripedium californicum, as indicated by previous interpretations based on morphological evidences. In addition, one pair of vicariant species, Cypripedium plectrochilum (eastern Asia) and Cypripedium arietinum (North America), unique to section Arietinum, was confirmed. Furthermore, within the monophyletic section Cypripedium two previously recognized subsections, Cypripedium and Macrantha, were shown to be paraphyletic. Our results suggested that this section split into two groups based on distribution (North America vs. Eurasia) instead of such previously used, morphological traits as flower color, and the shape of the lips (labellum) and lateral petals.     

Geographical origin of Leucobryum boninense Sull. & Lesq. (Leucobryaceae,Musci) endemic to the Bonin Islands,Japan

Leucobryum boninense is endemic to the Bonin Islands, Japan, and its related species are widely distributed in Asia and the Pacific. We aimed to clarify the phylogenetic relationships among Leucobryum species and infer the origin of L. boninense. We also describe the utility of the chloroplast trnK intron including matK for resolving the phylogenetic relationships among Leucobryum species, as phylogenetic analyses using trnK intron and/or matK have not been performed well in bryophytes to date. Fifty samples containing 15 species of Leucobryum from Asia and the Pacific were examined for six chloroplast DNA regions including rbcL, rps4, partial 5′ trnK intron, matK, partial 3′ trnK intron, and trnL‐F intergenic spacer plus one nuclear DNA region including ITS. A molecular phylogenetic tree showed that L. boninense made a clade with L. scabrum from Japan, Taiwan and, Hong Kong; L. javense which is widely distributed in East and Southeast Asia, and L. pachyphyllum and L. seemannii restricted to the Hawaii Islands, as well as with L. scaberulum from the Ryukyus, Japan, Taiwan, and southeastern China. Leucobryum boninense from various islands of the Bonin Islands made a monophylic group that was closely related to L. scabrum and L. javense from Japan. Therefore, L. boninense may have evolved from L. scabrum from Japan, Taiwan, or Hong Kong, or L. javense from Japan. We also described the utility of trnK intron including matK. A percentage of the parsimony‐informative characters in trnK intron sequence data (5.8%) was significantly higher than that from other chloroplast regions, rbcL (2.4%) and rps4 (3.2%) sequence data. Nucleotide sequence data of the trnK intron including matK are more informative than other chloroplast DNA regions for identifying the phylogenetic relationships among Leucobryum species.     

The complete chloroplast genome sequence of the Chinese endemic species Sorbus setschwanensis (Rosaceae) and its phylogenetic analysis

Sorbus setschwanensis Koehne is a pinnate-leaved Sorbus s.str. species endemic to China with narrow distribution and intriguing phylogeny that needs wider attention. In this paper, the complete chloroplast (cp) genome of S. setschwanensis is reported, and its phylogenetic position is analyzed. The complete cp genome of S. setschwanensis is 160 064 bp in size with 36.50% GC content. It has a typical quadripartite structure including a pair of inverted repeat regions (IRs) of 26 378 bp that separates a large single copy (LSC) region of 86 013 bp and a small single copy (SSC) region of 19 295 bp. The cp genome encodes 108 genes, comprising 76 protein-coding genes, 28 tRNA genes and 4 rRNA genes. Additionally, 52 simple sequence repeats (SSRs) and 43 dispersed repeats were identified. Comparison of the whole cp genome with those of other Sorbus species showed an overall high degree of sequence similarity, but there are six highly variable regions (trnR-atpA, petN-psbM, ndhC-trnV, trnE-trnT, trnT-trnL and rpl32-trnL) located in intergenic spacers that may be useful as molecular markers in future population genetic and phylogenetic studies in the genus. Phylogenetic analyses based on 108 coding genes from 25 species in Rosaceae revealed that S. setschwanensis is nested within Sorbus sect. Sorbus together with other pinnately leaved species, but does not form a sister lineage to S. rufopilosa belonging to the same series Multijugae. Thus, the systematic position of S. setschwanensis and relationships with other species in the genus needs to be further studied.     

PHYLOGENETIC PLACEMENT OF BOTRYOCOCCUS BRAUNII (TREBOUXIOPHYCEAE) AND BOTRYOCOCCUS SUDETICUS ISOLATE UTEX 2629 (CHLOROPHYCEAE)1

The phylogenetic placement of four isolates of Botryococcus braunii Kützing and of Botryococcus sudeticus Lemmermann isolate UTEX 2629 was investigated using sequences of the nuclear small subunit (18S) rRNA gene. The B. braunii isolates represent the A (two isolates), B, and L chemical races. One isolate of B. braunii (CCAP 807/1; A race) has a group I intron at Escherichia coli position 1046 and isolate UTEX 2629 has group I introns at E. coli positions 516 and 1512. The rRNA sequences were aligned with 53 previously reported rRNA sequences from members of the Chlorophyta, including one reported for B. braunii (Berkeley strain). Phylogenetic trees were constructed using distance, weighted maximum parsimony, and maximum likelihood, and their reliability was estimated using bootstrap analysis for distance and parsimony and Bayesian inference for likelihood. All methods showed, with high bootstrap or credibility support, that the four isolates of B. braunii form a monophyletic group whose closest relatives are in the genus Choricystis in the Trebouxiophyceae, whereas the previously reported B. braunii sequence is from a member of the Chlamydomonadales in the Chlorophyceae and isolate UTEX 2629 is a member of the Sphaeropleales in the Chlorophyceae. Polyphyly of these sequences was confirmed by Kishino‐Hasegawa tests on artificial trees in which sequences were moved to a single lineage.     

Molecular cytogenetics and characterization of a ZZ/ZW sex chromosome system in Triportheus nematurus (Characiformes, Characidae)

Chromosomes of Triportheus nematurus, a fish species from family Characidae, were analyzed in order to establish the conventional karyotype, location of C-band positive heterochromatin, Ag-NORs, GC- and AT-rich sites, and mapping of 18S and 5S rDNA with fluorescence in situ hybridization (FISH). The diploid number found was 2n = 52 chromosomes in both males and females. However, the females presented a pair of differentiated heteromorphic chromosomes, characterizing a ZZ/ZW sex chromosome system. The Z chromosome was metacentric and the largest one in the karyotype, bearing C-positive heterochromatin at pericentromeric and telomeric regions. The W chromosome was middle-sized submetacentric, appearing mostly heterochromatic after C-banding and presenting heterogeneous heterochromatin composed of GC- and AT-rich regions revealed by fluorochrome staining. Ag-NORs were also GC-rich and surrounded by heterochromatic regions, being located at the secondary constriction on the short arms of the second chromosome pair, in agreement with 18S rDNA sites detected with FISH. The 18S and 5S rDNA were aligned in tandem, representing an uncommon situation in fishes. The results obtained reinforce the basal condition of the ZZ/ZW sex system in the genus Triportheus, probably arisen prior to speciation in the group.     

Contrasting patterns of genetic structure in Caryocar (Caryocaraceae) congeners from flooded and upland Amazonian forests

In the present study, we compare the genetic structure of a flooded forest tree Caryocar microcarpum and a terra firme forest tree Caryocar villosum in the lower Rio Negro region and test the hypothesis that the Rio Negro, the largest tributary on the left bank of the Amazon River, has been acting as a geographical barrier to gene flow between populations from the left and right banks. Seventeen adult individuals on the left bank and 27 on the right bank of Rio Negro were sampled for C. microcarpum, whereas 27 on the left and 20 on the right bank were sampled for C. villosum. Two chloroplast DNA regions were sequenced: the intron of trnL gene and the intergenic region between psbA and trnH genes; and all individuals were genotyped using ten microsatellite loci. The trnL intron and psbA‐trnH intergenic spacer generated fragments of 459 bp and 424 bp, respectively. For C. microcarpum, six haplotypes were identified for trnL and seven for psbA‐trnH. By contrast, only one haplotype was found for C. villosum for both sequences. The results obtained showed that the Rio Negro has not been a barrier to gene flow by pollen and seeds for either species. No genetic differentiation and a high migration rate between populations from the left and right banks of the Rio Negro were detected for the chloroplast sequences and nuclear microsatellites, for both C. villosum and C. microcarpum. Although the two analysed sequences showed a sharp topology difference, both indicated that multiple lineages may have contributed to the origin of C. microcarpum populations in the Rio Negro basin. Nevertheless, for C. villosum, from terra firme, the results obtained may provide evidence of a recent expansion of one maternal lineage from an ancient relic population surviving in one of the few moist forest refuges of the Guiana Shield during extended droughts of the glacial periods. We hypothesize that the contrasting environments colonized by this congener pair may have played an important role in shaping the genetic structure of both species. © 2009 The Linnean Society of London, Biological Journal of the Linnean Society, 2009, 98 , 278–290.