Biogeographic diversification in Nolana （Solanaceae）, a ubiquitous member of the Atacama and Peruvian Deserts along the western coast of South America

The present paper reconstructs the biogeographic diversification for Nolana L.f. （Solanaceae）, a genus of 89 endemic species largely restricted to fog-dependent desert lomas formations of coastal Peru and Chile. Previous efforts have reconstructed a phylogenetic estimate for Nolana using a combination of molecular markers. Herein, we expand on those results to examine hypotheses of biogeographic origins and diversification patterns. Nolana occupies habitats within a continuous coastal desert and forms a terrestrial archipelago of discrete ＂islands＂ unique in size, topography, and species composition. Each locality contains at least one Nolana species and many contain multiple species in sympatry. The genus has a Chilean origin, with the basal clades confined to Chile with wide geographic and ecological distributions. Peru contains two strongly supported clades, suggesting two introductions with subsequent radiation. A Chilean clade of shrubby, small-flowered species appears to have had its origins from the same ancestors of the second line that radiated in Peru and northern Chile. Nolana galapagensis is endemic to the Islas Galapagos, with origins traced to Peruvian taxa with a divergence time of 0.35 mya. Rates of diversification over the past 4.02 mya in Nolana, in one of the driest habitats on Earth, suggest rapid adaptive radiation in several clades. Success in Nolana may be attributed to characters that confer a competitive advantage in unpredictable and water-dependent environments, such as succulent leaf anatomy and ecophysiology, and the reproductive mericarp unique to Nolana. The processes affecting or shaping the biota of western South America are discussed.     

Complex evolution in Arundinarieae (Poaceae: Bambusoideae): incongruence between plastid and nuclear GBSSI gene phylogenies

The monophyly of tribe Arundinarieae (the temperate woody bamboos) has been unequivocally recovered in previous molecular phylogenetic studies. In a recent phylogenetic study, 10 major lineages in Arundinarieae were resolved based on eight non-coding plastid regions, which conflicted significantly with morphological classifications both at the subtribal and generic levels. Nevertheless, relationships among and within the 10 lineages remain unclear. In order to further unravel the evolutionary history of Arundinarieae, we used the nuclear GBSSI gene sequences along with those of eight plastid regions for phylogenetic reconstruction, with an emphasis on Chinese species. The results of the plastid analyses agreed with previous studies, whereas 13 primary clades revealed in the GBSSI phylogeny were better resolved at the generic level than the plastid phylogeny. Our analyses also revealed many inconsistencies between the plastid DNA and the nuclear GBSSI trees. These results implied that the nuclear genome and the plastid genome had different evolutionary trajectories. The patterns of incongruence suggested that lack of informative characters, incomplete lineage sorting, and/or hybridization (introgression) could be the causes. Seven putative hybrid species were hypothesized, four of which are discussed in detail on the basis of topological incongruence, chromosome numbers, morphology, and distribution patterns, and those taxa probably resulted from homoploid hybrid speciation. Overall, our study indicates that the tribe Arundinarieae has undergone a complex evolution.     

Patterns of long-distance dispersal in Tiquilia subg. Tiquilia (Boraginaceae): implications for the origins of amphitropical disjuncts and Galapagos Islands endemics

Plant biogeographers have long argued whether plant disjunctions result from vicariance or dispersal. One of the classic patterns of plant disjunction involves New World amphitropical disjuncts, as exemplified by Tiquilia subg. Tiquilia (Boraginaceae). Subgenus Tiquilia forms a heterogeneous group of ~20 species that is amphitropically distributed in the deserts of North and South America, with four taxa endemic to the Galápagos Islands. The current study reconstructs the biogeographic history of subg. Tiquilia in order to explore the origins of New World amphitropical disjunction and of Galápagos endemism. A strongly supported phylogeny of the subgenus is estimated using sequence data from matK, ndhF, rps16, ITS, and waxy. Biogeographic analyses using combined and individual marker data sets reveal a complex history of long-distance dispersal in subg. Tiquilia. Biogeographic reconstructions imply a North American origin of the subgenus and its three major lineages and require at least four long-distance dispersal events to explain its current distribution. The South American taxa of subg. Tiquilia result from three independent and nonsimultaneous colonization events, while the monophyly and continental origins of the Galápagos endemics are unresolved. This study contributes to a growing body of evidence that intercontinental dispersal has been more common than previously realized.     

Understanding the colonization history of the Galápagos flycatcher (Myiarchus magnirostris)

The Galápagos archipelago has never been connected to any continental land masses, so it is of interest to know the colonization and diversification history of its endemic species. We analyzed the phylogenetic placement of the endemic Galápagos flycatcher, M. magnirostris, within Myiarchus by using the genes ND2 and cytb (1970 bp) to compare 16 of the 22 species that comprise this genus. We also analyzed variability in cytb sequences from 154 M. magnirostris individuals captured on seven Galápagos islands. Our phylogenetic analyses recovered the two main Myiarchus clades that had been described by previous genetic, morphological, and vocal analyses. M. magnirostris is monophyletic and its closest living relative is M. tyrannulus from Mexico and Central America. The average age for the split node between these two groups was approximately 850,000 years (95% C.I. 630,735-1,087,557). M. tyrannulus, M. nugator, M. nuttingi, M. sagrae, and M. stolidus are not monophyletic species. Within M. magnirostris itself, we found low nucleotide and haplotype diversities (π=0.0009 and h=0.4913, respectively) and a high genetic structure among populations. We also detected a star-shaped haplotype network and significantly negative values for Tajima's D and Fu's Fs for this species. Our results suggest that M. magnirostris originated from a single colonization event and had a recent population expansion in the Galápagos archipelago.     

Origin and population history of a recent colonizer, the yellow warbler in Galápagos and Cocos Islands

The faunas associated with oceanic islands provide exceptional examples with which to examine the dispersal abilities of different taxa and test the relative contribution of selective and neutral processes in evolution. We examine the patterns of recent differentiation and the relative roles of gene flow and selection in genetic and morphological variation in the yellow warbler (Dendroica petechia aureola) from the Galápagos and Cocos Islands. Our analyses suggest aureola diverged from Central American lineages colonizing the Galápagos and Cocos Islands recently, likely less than 300 000 years ago. Within the Galápagos, patterns of genetic variation in microsatellite and mitochondrial markers suggest early stages of diversification. No intra-island patterns of morphological variation were found, even across steep ecological gradients, suggesting that either (i) high levels of gene flow may be homogenizing the effects of selection, (ii) populations may not have had enough time to accumulate the differences in morphological traits, or (iii) yellow warblers show lower levels of 'evolvability' than some other Galápagos species. By examining genetic data and morphological variation, our results provide new insight into the microevolutionary processes driving the patterns of variation.     

Complete plastid genome sequences of Drimys, Liriodendron, and Piper : implications for the phylogenetic relationships of magnoliids

Background  

The magnoliids with four orders, 19 families, and 8,500 species represent one of the largest clades of early diverging angiosperms. Although several recent angiosperm phylogenetic analyses supported the monophyly of magnoliids and suggested relationships among the orders, the limited number of genes examined resulted in only weak support, and these issues remain controversial. Furthermore, considerable incongruence resulted in phylogenetic reconstructions supporting three different sets of relationships among magnoliids and the two large angiosperm clades, monocots and eudicots. We sequenced the plastid genomes of three magnoliids, Drimys (Canellales), Liriodendron (Magnoliales), and Piper (Piperales), and used these data in combination with 32 other angiosperm plastid genomes to assess phylogenetic relationships among magnoliids and to examine patterns of variation of GC content.     

Dealing with incongruence in the quest for the species tree: a case study from the orchid genus Satyrium

A species tree was reconstructed for the mainly African terrestrial orchid genus Satyrium. Separate phylogenetic analysis of both plastid and ribosomal nuclear DNA sequences for 63 species, revealed extensive topological conflict. Here we describe a detailed protocol to deal with incongruence involving three steps: identifying incongruence and testing its significance, assessing the cause of incongruence, and reconstructing the species tree. The Incongruence Length Difference test revealed that many cases of incongruence were non-significant. For the remaining significant cases, results from taxon jack-knifing experiments and parametric bootstrap suggested that non-biological artefacts such as sparse taxon sampling and long-branch attraction could be excluded as causes for the observed incongruence. In order to evaluate biological causes, such as orthology/paralogy conflation, lineage sorting, and hybridization, the number of events was counted that needs to be invoked a-posteriori to explain the observed pattern. In most cases where incongruence was significant, this resulted in a similar number of events for each of these different causes. Only for the three species from south east Asia, that form a monophyletic clade, hybridization was favoured over the alternative causes. This conclusion is based on the large number of events that needs to be invoked, in order for either orthology/paralogy conflation or lineage sorting to have been the cause of the incongruence+morphological evidence. The final species tree presented here is the product of the combined analysis of plastid and ITS sequences for all non-incongruent species and a-posteriori grafting of the incongruent clades or accessions onto the tree.     

Microsatellite primers for the four Galápagos mockingbird species (Mimus parvulus, Mimus macdonaldi, Mimus melanotis and Mimus trifasciatus)

Nineteen di- and tetranucleotide and one trinucleotide microsatellite DNA markers were isolated from the Galápagos mockingbird (Mimus parvulus) and tested for cross-species amplification in the other three mockingbird species in the Galápagos. In addition, primers for two microsatellite loci previously developed for Mimus polyglottos were redesigned to obtain shorter amplification fragments. The number of alleles per locus and species ranged from 1 to 8, and expected heterozygosity varied from 0.0 to 0.809. These microsatellite markers will be useful to study levels of inbreeding in different island populations.     

Characterization of 10 microsatellite loci in an avian louse, Degeeriella regalis (Phthiraptera: Ischnocera: Philopteridae)

We isolated and characterized 10 polymorphic microsatellite loci in an ischnoceran louse, Degeeriella regalis, which parasitizes the threatened Galápagos hawk (Buteo galapagoensis) and other falconiform birds. The loci were screened across 30 individuals from two island populations in the Galápagos Islands. The number of alleles per locus ranged from two to 28. Polymorphic information content ranged from 0.14 to 0.94 and observed heterozygosity ranged from 0 to 0.67. These markers will be valuable in comparative population genetics studies in this species, which is the focus of a long-term population and disease ecology research program.     

Notes on Galápagos grenadiers (Pisces, Gadiformes, Macrouridae), with the description of a new species of Coryphaenoides

Two unusual specimens of the grenadier genus Coryphaenoides were collected by the deep-submersible vehicle Johnson Sea-Link off the Galápagos. Unlike any other member of the genus, the snout in these specimens was rounded, non-protruding, naked anteriorly and ventrally, with no tubercular scales marking the terminal and lateral angles. They are herein described as Coryphaenoides gypsochilus. Additional specimens of grenadiers were procured by the Johnson Sea-Link, including the second and third specimens of Nezumia ventralis and the first record of Caelorinchus canus from these waters. Three species and one subspecies of Galápagos grenadiers are endemic.     

Colonization and diversification of Galápagos terrestrial fauna: a phylogenetic and biogeographical synthesis

Remote oceanic islands have long been recognized as natural models for the study of evolutionary processes involved in diversification. Their remoteness provides opportunities for isolation and divergence of populations, which make islands remarkable settings for the study of diversification. Groups of islands may share a relatively similar geological history and comparable climate, but their inhabitants experience subtly different environments and have distinct evolutionary histories, offering the potential for comparative studies. A range of organisms have colonized the Galápagos Islands, and various lineages have radiated throughout the archipelago to form unique assemblages. This review pays particular attention to molecular phylogenetic studies of Galápagos terrestrial fauna. We find that most of the Galápagos terrestrial fauna have diversified in parallel to the geological formation of the islands. Lineages have occasionally diversified within islands, and the clearest cases occur in taxa with very low vagility and on large islands with diverse habitats. Ecology and habitat specialization appear to be critical in speciation both within and between islands. Although the number of phylogenetic studies is continuously increasing, studies of natural history, ecology, evolution and behaviour are essential to completely reveal how diversification proceeded on these islands.     

War of the Iguanas: conflicting molecular and morphological phylogenies and long-branch attraction in iguanid lizards

Recent studies based on different types of data (i.e., morphology, molecules) have found strongly conflicting phylogenies for the genera of iguanid lizards but have been unable to explain the basis for this incongruence. We reanalyze published data from morphology and from the mitochondrial ND4, cytochrome b, 12S, and 16S genes to explore the sources of incongruence and resolve these conflicts. Much of the incongruence centers on the genus Cyclura, which is the sister taxon of Iguana, according to parsimony analyses of the morphology and the ribosomal genes, but is the sister taxon of all other Iguanini, according to the protein-coding genes. Maximum likelihood analyses show that there has been an increase in the rate of nucleotide substitution in Cyclura in the two protein-coding genes (ND4 and cytochrome b), although this increase is not as clear when parsimony is used to estimate branch lengths. Parametric simulations suggest that Cyclura may be misplaced by the protein-coding genes as a result of long-branch attraction; even when Cyclura and Iguana are sister taxa in a simulated phylogeny, Cyclura is still placed as the basal member of the Iguanini by parsimony analysis in 55% of the replicates. A similar long-branch attraction problem may also exist in the morphological data with regard to the placement of Sauromalus with the Galápagos iguanas (Amblyrhynchus and Conolophus). The results have many implications for the analysis of diverse data sets, the impact of long branches on parsimony and likelihood methods, and the use of certain protein-coding genes in phylogeny reconstruction.     

Development of 10 highly-polymorphic microsatellite markers in the vulnerable Galápagos land iguanas (genus Conolophus)

The two species of Galápagos land iguanas (Conolophus subcristatus and C. pallidus) are listed as 'vulnerable' species by the International Union for the Conservation of Nature (IUCN Red List; http://www.iucnredlist.org). Here, we report on the isolation and characterization of 10 microsatellite markers using 562 individuals sampled on all Galápagos islands where Conolophus species occur today. We show that these 10 loci are highly polymorphic and display diagnostic alleles for five out of the six island populations. These markers will be useful for Conolophus population genetic analyses as well as for guiding ongoing captive breeding programmes.     

Phylogenetic relationships in Myrceugenia (Myrtaceae) based on plastid and nuclear DNA sequences

Myrceugenia is a genus endemic to South America with a disjunct distribution: 12 species occurring mainly in central Chile and approximately 25 in southeastern Brazil. Relationships are reconstructed within Myrceugenia from four plastid markers (partial trnK-matK, rpl32-trnL, trnQ-5'rps16 and rpl16) and two ribosomal nuclear regions (ETS and ITS) using maximum parsimony and Bayesian analyses. Relationships inferred previously from morphological data are not completely consistent with those from molecular data. All molecular analyses support the hypothesis that Myrceugenia is monophyletic, except for M. fernadeziana that falls outside the genus. Chilean species and Brazilian species form two separate lineages. Chilean species form three early diverging clades, whereas Brazilian species are a strongly supported monophyletic group in a terminal position. Least average evolutionary divergence, low resolution, short branches, and high species diversity found in the Brazilian clade suggest rapid radiation. Geographical distributions and phylogenetic reconstructions suggest that extant Myrceugenia species arose in northern Chile followed by colonization southward and finally to the Juan Fernández Islands and southeastern Brazil.     

Wrasses of the Galápagos Islands, with the description of a new deepwater species of Halichoeres (Perciformes: Labridae)

Halichoeres raisneri, new species, is described from three specimens captured by the Johnson Sea Link submersible at 114-125 m off Wolf Island, Galápagos. Distinctive features of the new species include a dorsally projecting fleshy flap along the posterior three-quarters of the upper lip and the absence of a canine tooth at the corner of the upper jaw. The body color of freshly caught females is pale pink with two yellow stripes and five prominent pink spots above the uppermost stripe. Similarities between the new species and other labrids are discussed, and a key to the 16 nominal species of Labridae known from the Galápagos Islands is provided. Decodon melasma is recorded from the Archipelago for the first time.     

A phytosociological interpretation of vegetation from sandy hills of the Peruvian desert

The vegetation of the sandy hills ("lomas") constitutes the main originality of the Peruvian and Chilean desert with a high number of endemics that shapes the vicarious associations. In this work, a phytosociological view of sandy environments of the Peruvian coastal desert is presented. According to the Braun-Blanquet method, we have made up 32 phytosociological inventories and added 138 ones from others authors. In each inventory, we have analyzed its floristic composition and ecological parameters, as altitude, soil and geomorphology. All releves were synthesized in a table to deduce the different associations, higher phytosociological units, and the distribu tion of its flora along the Peruvian coast and the Andean Cordillera. Using the Shannon-Wiener diversity index, the diversity of this flora is discussed making a comparison with historical data about the use of the territory with livestock during pre-Inca and Inca cultures, and Spanish invasion. As a result, two associations from Southern Peru -Nolanetum scaposo-spathulatae and Palauetum camanensis-weberbaueri-, two alliances -Nolanion humifusae from central Peru, and Nolanion spathulatae from the Southern Peru- and a new order -Tetragonio crystallinae-Plantaginetalia limensis- are described. In Nolanetum scaposo-spathulatae, Dictyophragnus englerianus, Leptoglossis lomana, Nolana scaposa, N. spathulata, Palaua velutina and Tetragonia vestita are the main characteristics, while in Palauetum camanensis-weberbaueri association N. scaposa and P. velutina are replaced by Palaua camanensis and P. weberbaueri. Nolanion humifusae alliance integrates species as Geranium limae, Hymenocallis amancaes, Nolana humifusa, N. latipes, Palaua rhombifolia or Villanova oppositifolia. Likewise, Cistanthe weberbaueri, Cryptantha parviflora, Hoffmannseggia miranda, Lupinus mollendoensis, Nolana confinis, N. pallidula, N. scaposa, N. spathulata, Palaua camanensis, P. velutina, P. weberbaueri, Tetragonia vestita and Weberbauerella brongniartioides are the characteristic species of Nolanion spathulatae alliance. The Tetragonio crystallinae-Plantaginetalia limensis order presents characteristic plants don't linked with eutrophic soils, as Calandrinia alba, Cryptantha limensis, Dyschoriste repens, Monnina macrostachya, Oxalis lomana, Palaua malvifolia, Pectocarya lateriflora, Plantago limensis or Tetragonia crystallina, with a distribution that claps the geographical area of the new alliances. On the other hand, the vegetation of the desert ravines is discussed in the context of the coastal river plant communities and its disturbance by the dunes. After the application of the Shannon-Wiener diversity index on the synthetic table columns, we can deduce that an increase in Andean and European ruderal species is linked to an intensive livestock activity. The transhumance between the Andes and the coast from pre-Inca times until now, produces the plant dispersion of high Andean plants toward the coast; the Spanish colonization was the origin of the presence of European plants in the "lomas" vegetation of Peru.     

Phylogenetics of Anthyllis (Leguminosae: Papilionoideae: Loteae): Partial incongruence between nuclear and plastid markers, a long branch problem and implications for morphological evolution

Phylogenetic relationships in the genus Anthyllis (Leguminosae: Papilionoideae: Loteae) were investigated using data from the nuclear ribosomal internal transcribed spacer regions (ITS) and three plastid regions (psbA-trnH intergenic spacer, petB-petD region and rps16 intron). Bayesian and maximum parsimony (MP) analysis of a concatenated plastid dataset recovered well-resolved trees that are topologically similar, with many clades supported by unique indels. MP and Bayesian analyses of the ITS sequence data recovered trees that have several well-supported topological differences, both among analyses, and to trees inferred from the plastid data. The most substantial of these concerns A. vulneraria and A. lemanniana, whose placement in the parsimony analysis of the ITS data appears to be due to a strong long-branch effect. Analysis of the secondary structure of the ITS1 spacer showed a strong bias towards transitions in A. vulneraria and A. lemanniana, many of which were also characteristic of certain outgroup taxa. This may contribute to the conflicting placement of this clade in the MP tree for the ITS data. Additional conflicts between the plastid and ITS trees were more taxonomically focused. These differences may reflect the occurrence of reticulate evolution between closely related species, including a possible hybrid origin for A. hystrix. The patterns of incongruence between the plastid and the ITS data seem to correlate with taxon ranks. All of our phylogenetic analyses supported the monophyly of Anthyllis (incl. Hymenocarpos). Although they are often taxonomically associated with Anthyllis, the genera Dorycnopsis and Tripodion are shown here to be more closely related to other genera of Loteae. We infer up to six major clades in Anthyllis that are morphologically well-characterized, and which could be recognized as sections. Four of these agree with various morphology-based classifications, while the other two are novel. We reconstruct the evolution of several morphological characteristics found only in Anthyllis or tribe Loteae. Some of these characters support major clades, while others show evidence of homoplasy within Anthyllis.     

Viburnum phylogeny: evidence from the duplicated nuclear gene GBSSI

DNA sequencing studies of the granule-bound starch synthase gene (GBSSI) indicate the presence of two loci in Viburnum. Gene trees from separate and combined phylogenetic analyses of the GBSSI paralogues are generally congruent with each other and with trees from previous analyses, especially those of Donoghue et al. [Syst. Bot. 29 (2004) 188] based on nuclear ribosomal ITS and chloroplast trnK intron DNA sequences. Specifically, our GBSSI trees confirm (i) the monophyly of some and non-monophyly of other traditionally recognized taxonomic sections, (ii) the presence of three major supra-sectional lineages within Viburnum, and (iii) the resolution of many species relationships within the section-level clades. Analyses of GBSSI also provide greater resolution of relationships within the largest supra-sectional lineage. Relationships at the base of the Viburnum phylogeny remain uncertain; in particular, the position of the root, relationships among the supra-sectional clades, and the exact placement of several smaller groups (e.g., Viburnum clemensiae, Viburnum urceolatum, and section Pseudotinus). In two lineages each GBSSI paralogue is represented by two distinct sequences. The presence of additional copies appears to be correlated with polyploidy in these clades. Placement of the homoeologues in our gene trees suggests the possibility of a hybrid origin for these polyploids.     

Status of the eastern Pacific agujon needlefish Tylosurus pacificus (Steindachner, 1876) (Beloniformes: Belonidae)

Tylosurus pacificus (Steindachner, 1876) is confirmed to have full species rank based on: 1) sympatry with T. acus melanotus at Isla Gorgona and in Panamá; 2) level of morphological differentiation in numbers of vertebrae, dorsal and anal fin rays; and 3) level of mtDNA differentiation. The eastern Pacific agujon needlefish is found from the Gulf of California, Mexico, to Peru, including the Galápagos Islands.     

Redescription of Symphurus diabolicus, a poorly-known, deep-sea tonguefish (Pleuronectiformes: Cynoglossidae) from the Galápagos Archipelago

Symphurus diabolicus, previously known only from the holotype collected in 501 m west of Isla San Cristobal (Chatham Island), Galápagos Archipelago, is re-described based on the holotype (112.6 mm SL) and 19 additional specimens (61.1-123.5 mm SL) recently collected from deep waters around the Galápagos Archipelago. Symphurus diabolicus is characterized by: an elongate body; narrow head with pointed snout; 1-3-2 ID pattern; 106-110 dorsal-fin rays; 89-96 anal-fin rays; 12 caudal-fin rays; 57-59 total vertebrae; 5 hypurals; extremely small scales; no pupillary operculum; large, prominent eyes, with migrated eye near dorsal margin of head; relatively short postorbital head length; relatively long snout and predorsal lengths; black peritoneum visible through abdominal wall on both sides of body; uniform olive green to dark brown ocular-side coloration with series of prominent, darker brown, elliptical to rectangular, blotches (not usually forming crossbands) along body at bases of dorsal and anal fins; and uniformly whitish or light yellow blind side. Symphurus diabolicus appears to be endemic to the Galápagos Archipelago, and is relatively common (captured at 16 different localities) at depths of 308 to 757 m (observed as shallow as 245 m) in this region. Examination of this expanded series of specimens confirms the validity of S. diabolicus and provides characters to distinguish it from S. microlepis Garman, a similar species known only from the holotype taken at approximately 530 m off Pacific Panama.