Literatura Reciente sobre Filogenetica

Putting biogeography’s cart back behind taxonomy’s horse: a response to Triantis et al.

Thu, 17 May 2012 08:39:34 PDT

Abstract

In a recent paper, two of us discussed diversity patterns and diversification processes in the Azores flora. Triantis et al. (2012, Journal of Biogeography, 39, 1179–1184) challenged our hypothesis that palaeoclimatic differences had an effect on diversification rates and suggested that area, island age and isolation explain diversity patterns. They did not, however, fully address the results from our subsequent paper, in which we showed that diversity patterns evident from phylogeographic studies differ markedly from those suggested by checklists. Checklists are working hypotheses and we suggest that the discrepancies evident between molecular data and checklists may be indicative of deficiencies in our taxonomic understanding of the Azores flora. Patterns of molecular and morphological diversity need to be better understood, and the discrepancies between checklists and molecular data accounted for, before we can establish the relative importance of factors such as palaeoclimate, area, island age or isolation in generating endemic diversity patterns in the Azores flora.

Palaeobiodiversity and taxonomic resolution: linking past trends with present patterns

Valentí Rull — Thu, 17 May 2012 08:39:34 PDT

Evolutionary biogeography of Chile

Juan J. Morrone — Thu, 17 May 2012 04:47:36 PDT

Exploring a key synapomorphy: correlations between structure and function in the sternum V glands of Trichoptera and Lepidoptera (Insecta)

MARIE DJERNÆS, FELIX A. H. SPERLING — Fri, 18 May 2012 03:34:17 PDT

The sternum V glands are a key synapomorphy that unites Trichoptera with Lepidoptera, but their functional aspects have not been analysed from an evolutionary perspective. We examine phylogenetic trends and correlations between chemical and morphological features of these glands. The most likely ancestral gland compounds are heptan-2-ol, 4-hepten-2-one and -ol, nonan-2-one, and 6-nonen-2-one and -ol, making pheromone production a plausible ancestral function. The most widespread gland compounds (heptan-2-one and -ol and nonan-2-one and -ol) are not known from Apataniidae + Limnephilidae (Trichoptera), which in turn uniquely produce a number of methylated 3-ketones and their corresponding alcohols, probably functioning as pheromones. We propose a functional connection between perforated patches on sternum IV in females and a scaly/dome-covered area around the gland openings, as well as between perforated patches and lack of Trichoptera-type opening muscles. We also propose a functional connection between the shape of the gland reservoirs and the presence of gland reservoir musculature. The perforated patches were significantly correlated with several gland compounds that had double bonds between carbon atoms: the double bonds may lower the viscosity of the compounds, facilitating secretion through the tiny pores of the perforated patches. The production of defensive substances in Pycnopsyche (Trichoptera: Limnephilidae) is probably connected to the presence of large, compartmentalized gland reservoirs. Large glands in male Hydropsyche (Trichoptera: Hydropsychidae) are probably linked to male aggregation pheromone production. The relative sizes of sternum V gland reservoirs and fenestral gland reservoirs in female philopotamids (Trichoptera) suggest a complementary function of the two structures. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, ••, ••–••.

Phylogeny and systematics of Melanesia’s most diverse gecko lineage (Cyrtodactylus, Gekkonidae, Squamata)

Paul M. Oliver, Stephen J. Richards, Mark Sistrom — Tue, 15 May 2012 21:28:59 PDT

Oliver, P.M., Richards, S.J. & Sistrom, M. (2012). Phylogeny and systematics of Melanesia’s most diverse gecko lineage (Cyrtodactylus, Gekkonidae, Squamata). —Zoologica Scripta, 00, 000–000.

The systematics and biogeographical history of the diverse fauna of New Guinea and surrounding islands (Melanesia) remain poorly known. We present a phylogeny for 16 of the 21 recognised Melanesian bent-toed geckos in the genus Cyrtodactylus based on mitochondrial sequence data. These analyses reveal two divergent lineages of Cyrtodactylus within Melanesia. One includes a single recognised species with clear affinities to sampled taxa from Asia. The other comprises a relatively diverse radiation (likely 30+ species), not closely related to sampled extralimital taxa and centred on the Melanesian region (including Australia). Many taxa within this second lineage are endemic to islands surrounding New Guinea, and dispersal and speciation on peripheral islands appears to have played an important role in the accumulation of species diversity within this clade. In contrast, little diversity is centred upon montane areas, although we do identify at least one lineage closely associated with hill and lower montane forest that probably dates to at least the late Miocene. Our phylogenetic analyses also reveal numerous divergent lineages that require taxonomic attention, including at least two widespread taxa that are likely to be composite, additional specimens of Cyrtodactylus capreoloides (until recently known only from the holotype) and several divergent and completely novel lineages, two of which we introduce herein: Cyrtodactylus arcanus sp. n. and Cyrtodactylus medioclivus sp. n.

Phylogeny of mosquitoes of tribe Culicini (Diptera: Culicidae) based on morphological diversity

Thu, 17 May 2012 21:55:23 PDT

Harbach, R. E., Kitching, I. J., Culverwell, C. L., Dubois, J. & Linton, Y.-M. (2012). Phylogeny of mosquitoes of tribe Culicini (Diptera: Culicidae) based on morphological diversity. —Zoologica Scripta, 00, 000–000.

Relationships among taxa of the mosquito tribe Culicini are explored using 169 morphological characters from 86 exemplar species representing the four genera and 26 subgenera of Culicini, most species groups and subgroups of subgenus Culex and an outgroup of five species from five other tribes. We analysed the data set, with multistate characters treated as unordered, under implied weights with values of K ranging from 1 to 20, implemented by TNT. Each analysis, except K = 4, produced a single most parsimonious (fittest) cladogram (MPC). The topology of the ingroup was identical for K = 6–11, whereas the MPCs for K = 14–20 differed only in the position of a single species, which occupied the same position in the K = 16 and K = 6–11 topologies. The K = 9 and K = 16 trees were given further consideration. In both these cladograms, Lutzia is sister to a clade comprising genera Culex, Deinocerites and Galindomyia. The two topologies have 13 clades in common, but their arrangements differ primarily because of Culex (Culex) duttoni acting as a ‘rogue’ taxon. We evaluated the effect of removing this species from the K = 9 and K = 16 analyses and chose the refined K = 9 topology as the best hypothesis of relationships within Culicini. Genus Culex is not monophyletic because it includes Deinocerites and Galindomyia as derived members of the New World subgenera. With the exception of subgenera Culex, Eumelanomyia and Neoculex, there is strong support for the monophyly of all genera and subgenera. Subgenus Culex would be monophyletic were four other subgenera included and three other taxa (the Afrotropical Cx. duttoni, Neotropical Cx. apicinus and the Australasian Atriceps Group) excluded.

Alpine Crossroads or Origin of Genetic Diversity? Comparative Phylogeography of Two Sympatric Microgastropod Species

Alexander M. Weigand et al. — Mon, 14 May 2012 14:00:00 PDT

by Alexander M. Weigand, Markus Pfenninger, Adrienne Jochum, Annette Klussmann-Kolb

The Alpine Region, constituting the Alps and the Dinaric Alps, has played a major role in the formation of current patterns of biodiversity either as a contact zone of postglacial expanding lineages or as the origin of genetic diversity. In our study, we tested these hypotheses for two widespread, sympatric microgastropod taxa – Carychium minimum O.F. Müller, 1774 and Carychium tridentatum (Risso, 1826) (Gastropoda, Eupulmonata, Carychiidae) – by using COI sequence data and species potential distribution models analyzed in a statistical phylogeographical framework. Additionally, we examined disjunct transatlantic populations of those taxa from the Azores and North America. In general, both Carychium taxa demonstrate a genetic structure composed of several differentiated haplotype lineages most likely resulting from allopatric diversification in isolated refugial areas during the Pleistocene glacial periods. However, the genetic structure of Carychium minimum is more pronounced, which can be attributed to ecological constraints relating to habitat proximity to permanent bodies of water. For most of the Carychium lineages, the broader Alpine Region was identified as the likely origin of genetic diversity. Several lineages are endemic to the broader Alpine Region whereas a single lineage per species underwent a postglacial expansion to (re)colonize previously unsuitable habitats, e.g. in Northern Europe. The source populations of those expanding lineages can be traced back to the Eastern and Western Alps. Consequently, we identify the Alpine Region as a significant ‘hot-spot’ for the formation of genetic diversity within European Carychium lineages. Passive dispersal via anthropogenic means best explains the presence of transatlantic European Carychium populations on the Azores and in North America. We conclude that passive (anthropogenic) transport could mislead the interpretation of observed phylogeographical patterns in general.

Comparable Ages for the Independent Origins of Electrogenesis in African and South American Weakly Electric Fishes

Sébastien Lavoué et al. — Mon, 14 May 2012 14:00:00 PDT

by Sébastien Lavoué, Masaki Miya, Matthew E. Arnegard, John P. Sullivan, Carl D. Hopkins, Mutsumi Nishida

One of the most remarkable examples of convergent evolution among vertebrates is illustrated by the independent origins of an active electric sense in South American and African weakly electric fishes, the Gymnotiformes and Mormyroidea, respectively. These groups independently evolved similar complex systems for object localization and communication via the generation and reception of weak electric fields. While good estimates of divergence times are critical to understanding the temporal context for the evolution and diversification of these two groups, their respective ages have been difficult to estimate due to the absence of an informative fossil record, use of strict molecular clock models in previous studies, and/or incomplete taxonomic sampling. Here, we examine the timing of the origins of the Gymnotiformes and the Mormyroidea using complete mitogenome sequences and a parametric Bayesian method for divergence time reconstruction. Under two different fossil-based calibration methods, we estimated similar ages for the independent origins of the Mormyroidea and Gymnotiformes. Our absolute estimates for the origins of these groups either slightly postdate, or just predate, the final separation of Africa and South America by continental drift. The most recent common ancestor of the Mormyroidea and Gymnotiformes was found to be a non-electrogenic basal teleost living more than 85 millions years earlier. For both electric fish lineages, we also estimated similar intervals (16–19 or 22–26 million years, depending on calibration method) between the appearance of electroreception and the origin of myogenic electric organs, providing rough upper estimates for the time periods during which these complex electric organs evolved de novo from skeletal muscle precursors. The fact that the Gymnotiformes and Mormyroidea are of similar age enhances the comparative value of the weakly electric fish system for investigating pathways to evolutionary novelty, as well as the influences of key innovations in communication on the process of species radiation.

An Improved Likelihood Ratio Test for Detecting Site-Specific Functional Divergence among Clades of Protein-Coding Genes

Weadickand, C. J., Chang, B. S. W. — Tue, 15 May 2012 02:13:38 PDT

PartitionFinder: Combined Selection of Partitioning Schemes and Substitution Models for Phylogenetic Analyses

Lanfear, R., Calcott, B., Ho, S. Y. W., Guindon, S. — Tue, 15 May 2012 02:13:38 PDT

In phylogenetic analyses of molecular sequence data, partitioning involves estimating independent models of molecular evolution for different sets of sites in a sequence alignment. Choosing an appropriate partitioning scheme is an important step in most analyses because it can affect the accuracy of phylogenetic reconstruction. Despite this, partitioning schemes are often chosen without explicit statistical justification. Here, we describe two new objective methods for the combined selection of best-fit partitioning schemes and nucleotide substitution models. These methods allow millions of partitioning schemes to be compared in realistic time frames and so permit the objective selection of partitioning schemes even for large multilocus DNA data sets. We demonstrate that these methods significantly outperform previous approaches, including both the ad hoc selection of partitioning schemes (e.g., partitioning by gene or codon position) and a recently proposed hierarchical clustering method. We have implemented these methods in an open-source program, PartitionFinder. This program allows users to select partitioning schemes and substitution models using a range of information-theoretic metrics (e.g., the Bayesian information criterion, akaike information criterion [AIC], and corrected AIC). We hope that PartitionFinder will encourage the objective selection of partitioning schemes and thus lead to improvements in phylogenetic analyses. PartitionFinder is written in Python and runs under Mac OSX 10.4 and above. The program, source code, and a detailed manual are freely available from www.robertlanfear.com/partitionfinder.

Evolution of Bioluminescence in Marine Planktonic Copepods

Tue, 15 May 2012 02:13:38 PDT

Copepods are the dominant taxa in zooplankton communities of the ocean worldwide. Although bioluminescence of certain copepods has been known for more than a 100 years, there is very limited information about the structure and evolutionary history of copepod luciferase genes. Here, we report the cDNA sequences of 11 copepod luciferases isolated from the superfamily Augaptiloidea in the order Calanoida. Highly conserved amino acid residues in two similar repeat sequences were confirmed by the multiple alignment of all known copepod luciferases. Copepod luciferases were classified into two groups of Metridinidae and Heterorhabdidae/Lucicutiidae families based on phylogenetic analyses, with confirmation of the interrelationships within the Calanoida using 18S ribosomal DNA sequences. The large diversity in the specific activity of planktonic homogenates and copepod luciferases that we were able to express in mammalian cultured cells illustrates the importance of bioluminescence as a protective function against predators. We also discuss the relationship between the evolution of copepod bioluminescence and the aspects of their ecological characteristics, such as swimming activity and vertical habitat.

Concatenation and Concordance in the Reconstruction of Mouse Lemur Phylogeny: An Empirical Demonstration of the Effect of Allele Sampling in Phylogenetics

Tue, 15 May 2012 02:13:38 PDT

The systematics and speciation literature is rich with discussion relating to the potential for gene tree/species tree discordance. Numerous mechanisms have been proposed to generate discordance, including differential selection, long-branch attraction, gene duplication, genetic introgression, and/or incomplete lineage sorting. For speciose clades in which divergence has occurred recently and rapidly, recovering the true species tree can be particularly problematic due to incomplete lineage sorting. Unfortunately, the availability of multilocus or "phylogenomic" data sets does not simply solve the problem, particularly when the data are analyzed with standard concatenation techniques. In our study, we conduct a phylogenetic study for a nearly complete species sample of the dwarf and mouse lemur clade, Cheirogaleidae. Mouse lemurs (genus, Microcebus) have been intensively studied over the past decade for reasons relating to their high level of cryptic species diversity, and although there has been emerging consensus regarding the evolutionary diversity contained within the genus, there is no agreement as to the inter-specific relationships within the group. We attempt to resolve cheirogaleid phylogeny, focusing especially on the mouse lemurs, by employing a large multilocus data set. We compare the results of Bayesian concordance methods with those of standard gene concatenation, finding that though concatenation yields the strongest results as measured by statistical support, these results are found to be highly misleading. By employing an approach where individual alleles are treated as operational taxonomic units, we show that phylogenetic results are substantially influenced by the selection of alleles in the concatenation process.

Phylogeography and Population Dynamics of Dengue Viruses in the Americas

Tue, 15 May 2012 02:13:38 PDT

Changes in Dengue virus (DENV) disease patterns in the Americas over recent decades have been attributed, at least in part, to repeated introduction of DENV strains from other regions, resulting in a shift from hypoendemicity to hyperendemicity. Using newly sequenced DENV-1 and DENV-3 envelope (E) gene isolates from 11 Caribbean countries, along with sequences available on GenBank, we sought to document the population genetic and spatiotemporal transmission histories of the four main invading DENV genotypes within the Americas and investigate factors that influence the rate and intensity of DENV transmission. For all genotypes, there was an initial invasion phase characterized by rapid increases in genetic diversity, which coincided with the first confirmed cases of each genotype in the region. Rapid geographic dispersal occurred upon each genotype's introduction, after which individual lineages were locally maintained, and gene flow was primarily observed among neighboring and nearby countries. There were, however, centers of viral diversity (Barbados, Puerto Rico, Colombia, Suriname, Venezuela, and Brazil) that were repeatedly involved in gene flow with more distant locations. For DENV-1 and DENV-2, we found that a "distance-informed" model, which posits that the intensity of virus movement between locations is inversely proportional to the distance between them, provided a better fit than a model assuming equal rates of movement between all pairs of countries. However, for DENV-3 and DENV-4, the more stochastic "equal rates" model was preferred.

The pathway of auxin biosynthesis in plants

Mano, Y., Nemoto, K. — Sun, 13 May 2012 22:52:57 PDT

The plant hormone auxin, which is predominantly represented by indole-3-acetic acid (IAA), is involved in the regulation of plant growth and development. Although IAA was the first plant hormone identified, the biosynthetic pathway at the genetic level has remained unclear. Two major pathways for IAA biosynthesis have been proposed: the tryptophan (Trp)-independent and Trp-dependent pathways. In Trp-dependent IAA biosynthesis, four pathways have been postulated in plants: (i) the indole-3-acetamide (IAM) pathway; (ii) the indole-3-pyruvic acid (IPA) pathway; (iii) the tryptamine (TAM) pathway; and (iv) the indole-3-acetaldoxime (IAOX) pathway. Although different plant species may have unique strategies and modifications to optimize their metabolic pathways, plants would be expected to share evolutionarily conserved core mechanisms for auxin biosynthesis because IAA is a fundamental substance in the plant life cycle. In this review, the genes now known to be involved in auxin biosynthesis are summarized and the major IAA biosynthetic pathway distributed widely in the plant kingdom is discussed on the basis of biochemical and molecular biological findings and bioinformatics studies. Based on evolutionarily conserved core mechanisms, it is thought that the pathway via IAM or IPA is the major route(s) to IAA in plants.

Forthcoming Article: Evolution of the RALF gene family in plants: gene duplication and selection patterns

(author unknown) — Tue, 15 May 2012 10:46:54 PDT

Taxonomy versus phylogeny: evolutionary history of marsh rabbits without hopping to conclusions

Rosanna M. Tursi, Phillip T. Hughes, Eric A. Hoffman — Fri, 11 May 2012 05:59:40 PDT

Abstract

Aim

To evaluate whether population genetic structure reflects taxonomic recognition of the endangered Lower Keys marsh rabbit (Sylvilagus palustris hefneri) and the two mainland subspecies.

Location

Southeastern United States.

Methods

We inferred phylogenetic relationships, population structure and genetic diversity within S. palustris using a mitochondrial gene (cytochrome b) and 10 microsatellite loci.

Results

The cytochrome b sequence data revealed taxonomy-phylogeography incongruence, and microsatellite data revealed moderate structure (F_ST = 0.22) with two genetic clusters recovered: one grouping the western Lower Keys, and the second grouping the eastern Lower Keys together with the mainland. Furthermore, island genetic diversity was not reduced relative to mainland populations (cyt b: π: t = −0.6952, P = 0.5651; h: t = −1.2053, P = 0.4305; microsatellite: H_E: t = −4.1201, P = 0.1313; AR: t = −2.3113, P = 0.2441).

Main conclusions

The taxonomy-phylogeny disparity reveals unknown aspects of the evolutionary history including an absence of contemporary dispersal barriers between the mainland subspecies and a more recent Lower Keys isolation than originally thought. Moreover, diversity patterns indicate that undocumented man-mediated transfers may contribute to current genetic structure between eastern Lower Keys and the mainland. Although subspecies designations were not confirmed, these findings support recognition of western Lower Keys populations as a distinct population segment under the Endangered Species Act.

Foonchewia guangdongensis gen. et sp. nov. (Rubioideae: Rubiaceae) and its systematic position inferred from chloroplast sequences and morphology

Hai-Zhen WEN, Rui-Jiang WANG — Fri, 11 May 2012 04:25:18 PDT

Abstract The new species, Foonchewia guangdongensis R. J. Wang & H. Z. Wen and the new monotypic genus Foonchewia R. J. Wang (Rubioideae, Rubiaceae), are described from eastern Guangdong, China. It is characterized by its subshrub habit, pentamerous and heterostylous flowers, 2–1ocular ovary with many ovules, and apically dehiscent capsules with numerous angulated seeds. Phylogenetic analysis of four chloroplast DNA regions (rbcL, rps16, ndhF, and atpB-rbcL) revealed that the new genus is nested in the Spermacoceae alliance and is sister to Dunnia. Morphological comparison between these two genera demonstrated that they had few synapomorphies; it was therefore inappropriate to classify the new genus in the existing tribe Dunnieae, and a new tribe, Foonchewieae R. J. Wang, is accordingly proposed.

Molecular phylogeny of African hinge-back tortoises (Kinixys): implications for phylogeography and taxonomy (Testudines: Testudinidae)

Fri, 11 May 2012 04:02:53 PDT

Abstract

We examine the phylogeography, phylogeny and taxonomy of hinge-back tortoises using a comprehensive sampling of all currently recognized Kinixys species and subspecies and sequence data of three mitochondrial DNA fragments (2273 bp: 12S rRNA, ND4 + adjacent DNA coding for tRNAs, cytb) and three nuclear loci (2569 bp: C-mos, ODC, R35). Combined and individual analyses of the two data sets using Bayesian and Maximum Likelihood methods suggest that the savannah species of Kinixys are paraphyletic with respect to the rainforest species K. homeana and K. erosa, and that the rainforest species may be derived from a savannah-living ancestor. The previously recognized savannah species K. belliana was a conglomerate of three deeply divergent clades that we treat here as distinct species. We restrict the name K. belliana (Gray, 1830) to hinge-back tortoises ranging from Angola to Burundi, while five-clawed hinge-back tortoises from the northernmost part of the formerly recognized range of K. belliana, together with four-clawed tortoises from West Africa, are assigned to the species K. nogueyi (Lataste, 1886). These two species are allied to K. spekii, whereas Southeast African and Malagasy hinge-back tortoises formerly lumped together with K. belliana represent the distinct species K. zombensis Hewitt, 1931, which is sister to K. lobatsiana. The latter two species together constitute the sister group of the rainforest species K. homeana and K. erosa. Mitochondrial data suggest that K. natalensis has a basal phylogenetic position in a clade embracing K. belliana sensu stricto, K. nogueyi and K. spekii, while nuclear data and the two data sets combined favour a sister group relationship of K. natalensis to all other hinge-back tortoises. Phylogeographic structure is present in all wide-ranging species and correlates in K. homeana and K. erosa with the Dahomey Gap and former rainforest refugia. The Malagasy population of K. zombensis is weakly differentiated from its South African conspecifics and further sampling is needed to determine whether there is support for the subspecific distinctness of Malagasy tortoises.

Nelson’s arrested development

James S. Farris — Thu, 10 May 2012 09:42:04 PDT

DEEP DIVERSIFICATION AND LONG-TERM PERSISTENCE IN THE SOUTH AMERICAN ‘DRY DIAGONAL’: INTEGRATING CONTINENT-WIDE PHYLOGEOGRAPHY AND DISTRIBUTION MODELING OF GECKOS

Fri, 25 May 2012 20:45:22 PDT

The relative influence of Neogene geomorphological events and Quaternary climatic changes as causal mechanisms on Neotropical diversification remains largely speculative, as most divergence timing inferences are based on a single locus and have limited taxonomic or geographic sampling. To investigate these influences, we use a multilocus (two mitochondrial and 11 nuclear genes) range-wide sampling of Phyllopezus pollicaris, a gecko complex widely distributed across the poorly studied South American ‘dry diagonal’ biomes. Our approach couples traditional and model-based phylogeography with geospatial methods, and demonstrates Miocene diversification and limited influence of Pleistocene climatic fluctuations on P. pollicaris. Phylogeographic structure and distribution models highlight that persistence across multiple isolated regions shaped the diversification of this species complex. Approximate Bayesian computation supports hypotheses of allopatric and ecological/sympatric speciation between lineages that largely coincide with genetic clusters associated with Chaco, Cerrado, and Caatinga, standing for complex diversification between the ‘dry diagonal’ biomes. We recover extremely high genetic diversity and suggest that eight well-supported clades may be valid species, with direct implications for taxonomy and conservation assessments. These patterns exemplify how low-vagility species complexes, characterized by strong genetic structure and pre-Pleistocene divergence histories, represent ideal radiations to investigate broad biogeographic histories of associated biomes.