Process partitions, congruence, and the independence of characters: inferring relationships among closely related Hawaiian Drosophila from multiple gene regions

Investigating the genetic diversity and presence of forensically informative nucleotide sequences in Indian antelope (Antilope cervicapra) using multiple genes of the mitochondrial genome

Indian antelope or Blackbuck (Antilope cervicapra) is one of the widely distributed endemic species in India among wild bovids and a majority of preferred habitats are in human-dominated landscapes. Poaching threats and habitat degradation are major factors for the decline in Blackbuck population from its distribution range. Till date, there is no detailed study using molecular techniques in India on Blackbuck, except a few studies entailing phylogenetic scenario based on inadequate sampling and DNA sequences restricted over limited geographic areas. In view of this, the present study is aimed to screen the Blackbuck samples from a large part of its distribution range and to investigate the genetic diversity as well as to identify the forensically informative nucleotide sequences (FINS) for species identification. We relied on multi-genes approach using three genes of mtDNA genome viz. Cytochrome Oxidase I, Cytochrome b and 16S rRNA and identified the FINS in the Blackbuck population along with conspecific sequences divergence and genetic diversity indices. In all three genes, we observed 8 to 17 haplotypes with the intra-species sequence divergence of 0.004-0.016. Inter-species sequence divergence with the other closely related species of the Blackbuck was 0.0225-0.033. We report the presence of FINS across three genes from 12 to 18 and found more informative nucleotide sites using Cytochrome Oxidase I genes compared to Cytochrome b and 16S rRNA gene. We did not observe the presence of geographic-specific FINS amongst Blackbuck population that can be used to assign individuals to geographic origin. Besides, in the phylogenetic tree, samples from different locations did not cluster into geographic-specific clade and exhibited mixed homology for these sequences. We suggest exploring the feasibility of using nuclear markers for population assignment.

Missing data, clade support and "reticulation": the molecular systematics of Heliconius and related genera (Lepidoptera: Nymphalidae) re-examined

Kozak et al. (2015, Syst. Biol., 64: 505) portrayed the inference of evolutionary history among Heliconius and allied butterfly genera as a particularly difficult problem for systematics due to prevalent gene conflict caused by interspecific reticulation. To control for this, Kozak et al. conducted a series of multispecies coalescent phylogenetic analyses that they claimed revealed pervasive conflict among markers, but ultimately chose as their preferred hypothesis a phylogenetic tree generated by the traditional supermatrix approach. Intrigued by this seemingly contradictory set of conclusions, we conducted further analyses focusing on two prevalent aspects of the data set: missing data and the uneven contribution of phylogenetic signal among markers. Here, we demonstrate that Kozak et al. overstated their findings of reticulation and that evidence of gene-tree conflict is largely lacking. The distribution of intrinsic homoplasy and incongruence homoplasy in their data set does not follow the pattern expected if phylogenetic history had been obscured by pervasive horizontal gene flow; in fact, noise within individual gene partitions is ten times higher than the incongruence among gene partitions. We show that the patterns explained by Kozak et al. as a result of reticulation can be accounted for by missing data and homoplasy. We also find that although the preferred topology is resilient to missing data, measures of support are sensitive to, and strongly eroded by too many empty cells in the data matrix. Perhaps more importantly, we show that when some taxa are missing almost all characters, adding more genes to the data set provides little or no increase in support for the tree.

RECOGNIZING AND TESTING HOMOLOGY OF COURTSHIP DISPLAYS IN STORKS (AVES: CICONIIFORMES: CICONIIDAE)

Ethological studies in the 1940s and 1950s, most notably those of Lorenz and Tinbergen, emphasized a historical perspective. By the 1970s, the notion that behavioral traits are too plastic to retain historical information became prevalent, and evolutionary approaches in behavioral studies were largely abandoned. However, several recent studies have demonstrated that behavioral characters are remarkably consistent with phylogenies obtained from other data and not particularly prone to homoplasy. In this study, I coded descriptions of courtship display behaviors in stork species (Aves: Ciconiiformes: Ciconiidae) as a matrix of discrete characters. I mapped each behavioral character onto a phylogeny based on DNA-DNA hybridization distances to test the homology of individual characters. Generally, displays occurring early in courtship were congruent with phylogenetic relationships and showed little homoplasy, while displays occurring late in courtship were more homoplastic. I also performed a phylogenetic analysis of the behavioral data matrix using maximum parsimony. The strict consensus of the 24 most-parsimonious trees was congruent with the DNA-DNA hybridization tree in all nodes having greater than 70% bootstrap support.

Revised phylogenetic analysis of the Aetosauria (Archosauria: Pseudosuchia); assessing the effects of incongruent morphological character sets

Aetosauria is an early-diverging clade of pseudosuchians (crocodile-line archosaurs) that had a global distribution and high species diversity as a key component of various Late Triassic terrestrial faunas. It is one of only two Late Triassic clades of large herbivorous archosaurs, and thus served a critical ecological role. Nonetheless, aetosaur phylogenetic relationships are still poorly understood, owing to an overreliance on osteoderm characters, which are often poorly constructed and suspected to be highly homoplastic. A new phylogenetic analysis of the Aetosauria, comprising 27 taxa and 83 characters, includes more than 40 new characters that focus on better sampling the cranial and endoskeletal regions, and represents the most comprenhensive phylogeny of the clade to date. Parsimony analysis recovered three most parsimonious trees; the strict consensus of these trees finds an Aetosauria that is divided into two main clades: Desmatosuchia, which includes the Desmatosuchinae and the Stagonolepidinae, and Aetosaurinae, which includes the Typothoracinae. As defined Desmatosuchinae now contains Neoaetosauroides engaeus and several taxa that were previously referred to the genus Stagonolepis, and a new clade, Desmatosuchini, is erected for taxa more closely related to Desmatosuchus. Overall support for some clades is still weak, and Partitioned Bremer Support (PBS) is applied for the first time to a strictly morphological dataset demonstrating that this weak support is in part because of conflict in the phylogenetic signals of cranial versus postcranial characters. PBS helps identify homoplasy among characters from various body regions, presumably the result of convergent evolution within discrete anatomical modules. It is likely that at least some of this character conflict results from different body regions evolving at different rates, which may have been under different selective pressures.

Evidence of constant diversification punctuated by a mass extinction in the African cycads

The recent evidence that extant cycads are not living fossils triggered a renewed search for a better understanding of their evolutionary history. In this study, we investigated the evolutionary diversification history of the genus Encephalartos, a monophyletic cycad endemic to Africa. We found an antisigmoidal pattern with a plateau and punctual explosive radiation. This pattern is typical of a constant radiation with mass extinction. The rate shift that we found may therefore be a result of a rapid recolonization of niches that have been emptied owing to mass extinction. Because the explosive radiation occurred during the transition Pliocene–Pleistocene, we argued that the processes might have been climatically mediated.

New insights into the phylogenetic relationships, character evolution, and phytogeographic patterns of Calceolaria (Calceolariaceae)

Biogeographical patterns and diversification processes in Andean and Patagonian flora are not yet well understood. Calceolaria is a highly diversified genus of these areas, representing one of the most specialized plant-pollinator systems because flowers produce nonvolatile oils, a very unusual floral reward. Phylogenetic analyses with molecular (ITS and matK) and morphological characters from 103 Calceolaria species were conducted to examine relationships, to understand biogeographic patterns, and to detect evolutionary patterns of floral and ecological characters. Total evidence analysis retrieved three major clades, which strongly correspond to the three previously recognized subgenera, although only subgenus Rosula was retrieved as a monophyletic group. A single historical event explains the expansion from the southern to central Andes, while different parallel evolutionary lines show a northward expansion from the central to northern Andes across the Huancabamba Deflection, an important geographical barrier in northern Peru. Polyploidy, acquisition of elaiophores, and a nototribic pollination mechanism are key aspects of the evolutionary history of Calceolaria. Pollination interactions were more frequently established with Centris than with Chalepogenus oil-collecting bee species. The repeated loss of the oil gland and shifts to pollen as the only reward suggest an evolutionary tendency from highly to moderately specialized pollination systems.

Phylogenetic analysis of seven WRKY genes across the palm subtribe Attaleinae (Arecaceae) [corrected] identifies Syagrus as sister group of the coconut

BACKGROUND

The Cocoseae is one of 13 tribes of Arecaceae subfam. Arecoideae, and contains a number of palms with significant economic importance, including the monotypic and pantropical Cocos nucifera L., the coconut, the origins of which have been one of the "abominable mysteries" of palm systematics for decades. Previous studies with predominantly plastid genes weakly supported American ancestry for the coconut but ambiguous sister relationships. In this paper, we use multiple single copy nuclear loci to address the phylogeny of the Cocoseae subtribe Attaleinae, and resolve the closest extant relative of the coconut.

METHODOLOGY/PRINCIPAL FINDINGS

We present the results of combined analysis of DNA sequences of seven WRKY transcription factor loci across 72 samples of Arecaceae tribe Cocoseae subtribe Attaleinae, representing all genera classified within the subtribe, and three outgroup taxa with maximum parsimony, maximum likelihood, and Bayesian approaches, producing highly congruent and well-resolved trees that robustly identify the genus Syagrus as sister to Cocos and resolve novel and well-supported relationships among the other genera of the Attaleinae. We also address incongruence among the gene trees with gene tree reconciliation analysis, and assign estimated ages to the nodes of our tree.

CONCLUSIONS/SIGNIFICANCE

This study represents the as yet most extensive phylogenetic analyses of Cocoseae subtribe Attaleinae. We present a well-resolved and supported phylogeny of the subtribe that robustly indicates a sister relationship between Cocos and Syagrus. This is not only of biogeographic interest, but will also open fruitful avenues of inquiry regarding evolution of functional genes useful for crop improvement. Establishment of two major clades of American Attaleinae occurred in the Oligocene (ca. 37 MYBP) in Eastern Brazil. The divergence of Cocos from Syagrus is estimated at 35 MYBP. The biogeographic and morphological congruence that we see for clades resolved in the Attaleinae suggests that WRKY loci are informative markers for investigating the phylogenetic relationships of the palm family.

Resolution of the Hylobates phylogeny: congruence of mitochondrial D-loop sequences with molecular, behavioral, and morphological data sets

Gibbons of the genus Hylobates likely speciated very rapidly following isolation by rising sea levels during the Pleistocene. We sequenced the hypervariable region I (HV-I) of the mitochondrial D-loop to reconstruct the phylogeny of this group. Although the results clearly supported monophyly of each of the six species, the relationships among them were not clearly resolved by these data alone. A homogeneity test against published data sets of a coding mitochondrial locus (ND3-ND4 region), behavioral characters (vocalizations), and morphological traits (including skeletal and soft tissue anatomy) revealed no significant incongruence, and combining them resulted in a phylogenetic tree with much stronger support. The Kloss's gibbon (H. klossii), long considered a primitive taxon based on morphology, shares many molecular and vocal characteristics with the Javan gibbon (H. moloch), and appear as the most recently derived species. The northernmost species (H. lar and H. pileatus) are the most basal taxa. These data suggest that ancestral gibbons radiated from north to south. Unlike other markers, the HV-I region can accurately identify members of different gibbon species much like a DNA barcode, with potential applications to conservation.

Challenges of phylogenetic analyses of aDNA sequences

One of the crucial steps of authentication of aDNA sequences is phylogenetic consistency. Amplified sequences should fit into the phylogenetic framework of their supposed origin. An inherent property of aDNA sequences however, is their short sequence length. Additionally, genes for aDNA studies are often chosen by their preservation potential rather than by phylogenetically informative content. This poses potential challenges regarding their analyses, and might result in an inaccurate reflection of the supposed phylogenetic history of the sequence or organism under study. In this paper some fundamental problems of phylogenetic analysis and interpretation of aDNA datasets are discussed. Suggestions for character sampling and treatment of missing data are made. The publication is the result of a talk from the 1st PAMINSA Meeting in Rio de Janeiro, July 2005.

Homology assessment and molecular sequence alignment

Hypotheses of homology are the basis of phylogenetic analysis. All character data are considered to be equivalent regardless of the source of those characters. Putative homology statements are designated based on observations of similarity. Pairwise sequence alignment using the Needleman-Wunsch algorithm is the basis for similarity maximization between molecular sequences. Multiple sequence alignment uses this algorithm in a topologically hierarchical framework. The resulting hypotheses of homology are tested in conjunction with character congruence through parsimony. This review introduces some underlying principles of phylogenetic analysis as they pertain homology testing and DNA sequence alignment.

What’s in a character?

Systematic analyses are included as integral parts of bioinformatic analysis. The use of phenetic and phylogenetic trees in many of the newer areas of biology create a need for bioinformaticists to understand more completely the nuances of systematic analysis. Any description in comparative biology, universally begins with what information to use in the comparative endeavor. Phylogenetic approaches are no different. The diversity of approaches and phylogenetic questions in systematics have sometimes hindered a precise understanding of what primary data should be collected to perform such analyses. In addition, one should always keep in mind that the objective of systematic organization of entities in nature not only strives to organize those entities in an objective, repeatable and operational way, but also to organize the attributes of the entities in a similar hierarchical context. This paper attempts to describe characters as the basis of all comparative analysis, to describe the diverse kinds of primary data that exist today in biology, genomics, and bioinformatics, and to place these kinds of primary data in the context of the established approaches to tree building.

Sexual selection and speciation in hawaiian Drosophila

Many ideas about sexual selection and speciation have been stimulated by considering Hawaiian Drosophila. In turn, the ideas and models have stimulated research with the flies, particularly members of the planitibia group. This paper describes high points of some of the models and reviews data that are relevant to understanding sexual selection and speciation in this species group.

Phylogenetic relationships of the New World Troidini swallowtails (Lepidoptera: Papilionidae) based on COI, COII, and EF-1α genes

A phylogeny of the Neotropical members of the Tribe Troidini (Lepidoptera: Papilionidae) was obtained with sequences of three protein-coding genes: two mitochondrial (COI and COII), and one nuclear (EF-1alpha). Parsimony and Bayesian analyses of 33 taxa resulted in very similar trees regardless of method used with the 27 troidines always forming a monophyletic clade. Within Troidini, the genus Battus is sister group to the remaining troidines, followed by a clade formed by the Paleotropical taxa (here represented by three exemplars). The genus Euryades is the next branch, and sister group of Parides. The genus Parides is monophyletic, and is divided into four main groups by Maximum Parsimony analysis, with the most basal group composed of tailed species restricted to SE Brazil. Character optimization of ecological and morphological traits over the phylogeny proposed for troidines indicated that the use of several species of Aristolochia is ancestral over the use of few or a single host-plant. For the other three characters, the ancestral states were the absence of long tails, forest as the primary habitat and oviposition solitary or in loose group of several eggs.

Quantifying patterns in the evolution of reproductive isolation

We present a likelihood-based statistical method for examining the pattern or rate of evolution of reproductive isolation. The method uses large empirical datasets to estimate, for a given clade, the average duration of two phases in the divergence of populations. The first phase is a lag phase and refers to the period during which lineages diverge but no detectable reproductive isolation evolves. The second is an accumulation phase, referring to the period during which the magnitude of reproductive isolation between diverging lineages increases. The pattern of evolution is inferred from the relative durations of these two phases. Results of analyses of postzygotic isolation data indicate significant differences among taxa in the pattern of evolution of postzygotic isolation that are consistent with predictions based on genetic differences among these groups. We also examine whether the evolution of postzygotic isolation is best explained by either of two models for the rate of accumulation: a linear model or a quadratic function as may be suggested by recent studies. Our analysis indicates that the appropriateness of either model varies among taxa.

A molecular phylogeny of Amazona: implications for Neotropical parrot biogeography, taxonomy, and conservation

Amazon parrots (Genus Amazona) are among the most recognizable and imperiled of all birds. Several hypotheses regarding the evolutionary history of Amazona are investigated using a combined phylogenetic analysis of DNA sequence data from six partitions including mitochondrial (COI, 12S, and 16S) and nuclear (beta-fibint7, RP40, and TROP) regions. The results demonstrate that Amazona is not monophyletic with respect to the placement of the Yellow-faced parrot (Amazona xanthops), as first implied by. In addition, the analysis corroborates previous studies suggesting a Neotropical short-tailed parrot genus as sister to Amazona. At a finer level, the phylogeny resolves the Greater Antillean endemic species as constituting a monophyletic group, including the Central American Amazona albifrons, while further revealing a paraphyletic history for the extant Amazon species of the Lesser Antilles. The reconstructed phylogeny provides further insights into the mainland sources of the Antillean Amazona, reveals areas of taxonomic uncertainty within the genus, and presents historical information that may be included in conservation priority-setting for Amazon parrots.

Monophyly and relationships of wrens (Aves: Troglodytidae): a congruence analysis of heterogeneous mitochondrial and nuclear DNA sequence data

The wrens (Aves: Troglodytidae) are a group of primarily New World insectivorous birds, the monophyly of which has long been recognized, but whose intergeneric relationships are essentially unknown. In order to test the monophyly of the group, and to attempt to resolve relationships among genera within it, sequences from the mitochondrial cytochrome b gene and the fourth intron of the nuclear beta-fibrinogen gene were obtained from nearly all genera of wrens, from their relatives as suggested by traditional taxonomy and DNA-DNA hybridization analyses, and from additional passerines. Maximum likelihood analysis of the two data sets yielded maximal congruence between independently derived estimates of relationship, outperforming a variety of weighted parsimony methods. Hierarchical likelihood ratio tests indicated that the two gene regions differed significantly in every estimated parameter of sequence evolution, and combined analysis of the two data sets was accomplished using a heterogeneous-model Bayesian approach. Independent and simultaneous analyses of both data sets supported monophyly of the wrens (excluding one recently added member, the monotypic genus Donacobius) and a sister-group relationship between wrens and the gnatcatchers (Polioptila). Additionally, strong support was found for paraphyly of the genus Thryothorus, and for a sister-group relationship between the genera Cistothorus and Troglodytes. Analyses of these data failed to resolve basal relationships within wrens, possibly due to ambiguity in rooting with a distant, species-poor outgroup. Analysis of the combined data for wrens alone yielded results which were largely congruent with relationships inferred using the complete data set, with the benefit of stronger support for relationships within the group. However, alternative rootings of this ingroup tree were weakly supported by nucleotide substitution data. Insertion-deletion events suggest that the genus Salpinctes may be sister to all other wrens.

Molecular phylogeny of the gobioid fishes (Teleostei: Perciformes: Gobioidei)

The phylogeny of groups within Gobioidei is examined with molecular sequence data. Gobioidei is a speciose, morphologically diverse group of teleost fishes, most of which are small, benthic, and marine. Efforts to hypothesize relationships among the gobioid groups have been hampered by the prevalence of reductive evolution among goby species; such reduction can make identification of informative morphological characters particularly difficult. Gobies have been variously grouped into two to nine families, several with included subfamilies, but most existing taxonomies are not phylogenetic and few cladistic hypotheses of relationships among goby groups have been advanced. In this study, representatives of eight of the nine gobioid familes (Eleotridae, Odontobutidae, Xenisthmidae, Gobiidae, Kraemeriidae, Schindleriidae, Microdesmidae, and Ptereleotridae), selected to sample broadly from the range of goby diversity, were examined. Complete sequence from the mitochondrial ND1, ND2, and COI genes (3573 bp) was used in a cladistic parsimony analysis to hypothesize relationships among the gobioid groups. A single most parsimonious topology was obtained, with decay indices indicating strong support for most nodes. Major phylogenetic conclusions include that Xenisthmidae is part of Eleotridae, and Eleotridae is paraphyletic with respect to a clade composed of Gobiidae, Microdesmidae, Ptereleotridae, Kraemeriidae, and Schindleriidae. Within this five-family clade, two clades are recovered. One includes Gobionellinae, which is paraphyletic with respect to Kraemeriidae, Sicydiinae, Oxudercinae, and Amblyopinae. The other contains Gobiinae, also paraphyletic, and including Microdesmidae, Ptereleotridae, and Schindleriidae. Previous morphological evidence for goby groupings is discussed; the phylogenetic hypothesis indicates that the morphological reduction observed in many goby species has been derived several times independently.

Phylogenetic and expression analysis of the glutamate-receptor-like gene family in Arabidopsis thaliana

The ionotropic glutamate receptor (iGluR) gene family has been widely studied in animals and is determined to be important in excitatory neurotransmission and other neuronal processes. We have previously identified ionotropic glutamate receptor-like genes (GLRs) in Arabidopsis thaliana, an organism that lacks a nervous system. Upon the completion of the Arabidopsis genome sequencing project, a large family of GLR genes has been uncovered. A preliminary phylogenetic analysis divides the AtGLR gene family into three clades and is used as the basis for the recently established nomenclature for the AtGLR gene family. We performed a phylogenetic analysis with extensive annotations of the iGluR gene family, which includes all 20 Arabidopsis GLR genes, the entire iGluR family from rat (except NR3), and two prokaryotic iGluRs, Synechocystis GluR0 and Anabaena GluR. Our analysis supports the division of the AtGLR gene family into three clades and identifies potential functionally important amino acid residues that are conserved in both prokaryotic and eukaryotic iGluRs as well as those that are only conserved in AtGLRs. To begin to investigate whether the three AtGLR clades represent different functional classes, we performed the first comprehensive mRNA expression analysis of the entire AtGLR gene family. On the basis of RT-PCR, all AtGLRs are expressed genes. The three AtGLR clades do not show distinct clade-specific organ expression patterns. All 20 AtGLR genes are expressed in the root. Among them, five of the nine clade-II genes are root-specific in 8-week-old Arabidopsis plants.

A molecular phylogeny of Costaceae (Zingiberales)

The phylogenetic relationships of Costaceae, a tropical monocotyledonous family sister to the gingers (Zingiberaceae), were investigated with a combination of two chloroplast loci (the trnL-F locus, including the trnL intron, the 3'trnL exon, and the trnL-F intergenic spacer, and the trnK locus, including the trnK intron and the matK coding region) and one nuclear locus (ITS1-5.8s-ITS2). The resulting parsimony analysis of selected taxa that demonstrate the range of floral morphological variation in the family shows that the Cadalvena-type [corrected] floral morphology is ancestral to the group and that both Tapeinochilos species and a Monocostus + Dimerocostus clade represent recent divergences. The genus Costus is broadly paraphyletic but Costus subgenus Eucostus K. Schum. represents a large monophyletic radiation that is poorly resolved. Within this clade, secondary analyses suggest that pollination syndrome, traditionally used for taxonomic and classification purposes within the genus Costus, is a relatively plastic trait of limited phylogenetic utility. This represents the first detailed investigation into intrageneric and interspecific evolutionary relationships within the family Costaceae and presents some novel evolutionary trends with respect to floral morphology and biogeography.

Sources of incongruence among mammalian mitochondrial sequences: COII, COIII, and ND6 genes are main contributors

To investigate the origins of incongruence among mammalian mitochondrial protein-coding genes, we compiled a matrix that included 13 protein-coding-genes for 41 mammals from 14 different orders. This matrix was examined for congruence using different partitioning strategies. The incongruence length difference test showed significant incongruence among the 13 gene partitions used simultaneously, and the result was not affected by third codon or transversion weighting. In the pair-wise comparisons, significant incongruence was detected between NADH:ubiquinone oxidoreductase subunit 6 gene (ND6), cytochrome oxidase subunit II (COII), or cytochrome oxidase subunit III (COIII) gene partitioned individually against the rest of the genes. Omission of any of the 14 mammalian orders alone or in combinations from the matrix did not result in a statistically significant improvement of congruence, suggesting that taxonomic sampling will not improve congruence among the data sets. However, omission of the ND6, COII, and COIII significantly improved congruence in our data matrix. Possible origins of unusual phylogenetic properties of the three genes are discussed.

Mitochondrial DNA Evidence and Evolution in Varanoidea (Squamata)

Varanoidea is a monophyletic group of anguimorph lizards, comprising the New World helodermatids, the Bornean earless monitor Lanthanotus borneensis, and the Old World monitors (Varanus). I use mitochondrial DNA sequences and extensive taxonomic sampling to test alternative hypotheses of varanoid relationships. The most parsimonious hypothesis confirms the monophyly of Varanoidea (Heloderma, Lanthanotus, and Varanus) and Varanus, as well as the sister-taxon relationship of Varanus and Lanthanotus. The relationships among Varanus species differ in several respects from previous hypotheses. Three major lineages are recognized within Varanus: an African clade basal to the rest of the group, an Indo-Asian clade, and an Indo-Australian clade. Within the last lineage, the endemic Australian dwarf monitors (Odatria) form a clade sister to the large Australian monitors (the gouldii group). Tests of the effects of rate heterogeneity and homoplasy demonstrate that putative process partitions of data are largely congruent with one another and contribute positive support to the overall hypothesis.

The use of anonymous DNA markers in assessing worldwide relatedness in the yeast species Pichia kluyveri Bedford and Kudrjavzev

Pichia kluyveri, a sexual ascomycetous yeast from cactus necroses and acidic fruit, is divided into three varieties. We used physiological, RAPD, and AFLP data to compare 46 P. kluyveri strains collected worldwide to investigate relationships among varieties. Physiology did not place all strains into described varieties. Although the combined AFLP and RAPD data produced a single most parsimonious tree, separate analysis of AFLP and RAPD data resulted in significantly different trees (by the partition homogeneity test). We then compared the distribution of strains per band to an expected distribution. This suggested we could separate both the AFLP and RAPD datasets into bands from rapidly and slowly changing DNA regions. When only bands from slowly changing regions (from each dataset) were included in the analysis, both the RAPD and AFLP datasets supported a single tree. This second tree did not differ significantly from the cladogram based on all of the DNA data, which we accepted as the best estimate of the phylogeny of these yeast strains. Based on this phylogeny, we were able to demonstrate the strong influence of geography on the population structure of this yeast, confirm the monophyly of one variety, question the utility of maintaining another variety, and demonstrate that the physiological differences used to separate the varieties did not do so in all cases.

The current state of insect molecular systematics: a thriving Tower of Babel

Insect molecular systematics has undergone remarkable recent growth. Advances in methods of data generation and analysis have led to the accumulation of large amounts of DNA sequence data from most major insect groups. In addition to reviewing theoretical and methodological advances, we have compiled information on the taxa and regions sequenced from all available phylogenetic studies of insects. It is evident that investigators have not usually coordinated their efforts. The genes and regions that have been sequenced differ substantially among studies and the whole of our efforts is thus little greater than the sum of its parts. The cytochrome oxidase I, 16S, 18S, and elongation factor-1 alpha genes have been widely used and are informative across a broad range of divergences in insects. We advocate their use as standards for insect phylogenetics. Insect molecular systematics has complemented and enhanced the value of morphological and ecological data, making substantial contributions to evolutionary biology in the process. A more coordinated approach focused on gathering homologous sequence data will greatly facilitate such efforts.

Phylogeny of the bee genus Halictus (Hymenoptera: halictidae) based on parsimony and likelihood analyses of nuclear EF-1alpha sequence data

We investigated higher-level phylogenetic relationships within the genus Halictus based on parsimony and maximum likelihood (ML) analysis of elongation factor-1alpha DNA sequence data. Our data set includes 41 OTUs representing 35 species of halictine bees from a diverse sample of outgroup genera and from the three widely recognized subgenera of Halictus (Halictus s.s., Seladonia, and Vestitohalictus). We analyzed 1513 total aligned nucleotide sites spanning three exons and two introns. Equal-weights parsimony analysis of the overall data set yielded 144 equally parsimonious trees. Major conclusions supported in this analysis (and in all subsequent analyses) included the following: (1) Thrincohalictus is the sister group to Halictus s.l., (2) Halictus s.l. is monophyletic, (3) Vestitohalictus renders Seladonia paraphyletic but together Seladonia + Vestitohalictus is monophyletic, (4) Michener's Groups 1 and 3 are monophyletic, and (5) Michener's Group 1 renders Group 2 paraphyletic. In order to resolve basal relationships within Halictus we applied various weighting schemes under parsimony (successive approximations character weighting and implied weights) and employed ML under 17 models of sequence evolution. Weighted parsimony yielded conflicting results but, in general, supported the hypothesis that Seladonia + Vestitohalictus is sister to Michener's Group 3 and renders Halictus s.s. paraphyletic. ML analyses using the GTR model with site-specific rates supported an alternative hypothesis: Seladonia + Vestitohalictus is sister to Halictus s.s. We mapped social behavior onto trees obtained under ML and parsimony in order to reconstruct the likely historical pattern of social evolution. Our results are unambiguous: the ancestral state for the genus Halictus is eusociality. Reversal to solitary behavior has occurred at least four times among the species included in our analysis.

Dynamically heterogenous partitions and phylogenetic inference: an evaluation of analytical strategies with cytochrome b and ND6 gene sequences in cranes

ki ctes over whether molecular sequence data should be partitioned for phylogenetic analysis often confound two types of heterogeneity among partitions. We distinguish historical heterogeneity (i.e., different partitions have different evolutionary relationships) from dynamic heterogeneity (i.e., different partitions show different patterns of sequence evolution) and explore the impact of the latter on phylogenetic accuracy and precision with a two-gene, mitochondrial data set for cranes. The well-established phylogeny of cranes allows us to contrast tree-based estimates of relevant parameter values with estimates based on pairwise comparisons and to ascertain the effects of incorporating different amounts of process information into phylogenetic estimates. We show that codon positions in the cytochrome b and NADH dehydrogenase subunit 6 genes are dynamically heterogenous under both Poisson and invariable-sites + gamma-rates versions of the F84 model and that heterogeneity includes variation in base composition and transition bias as well as substitution rate. Estimates of transition-bias and relative-rate parameters from pairwise sequence comparisons were comparable to those obtained as tree-based maximum likelihood estimates. Neither rate-category nor mixed-model partitioning strategies resulted in a loss of phylogenetic precision relative to unpartitioned analyses. We suggest that weighted-average distances provide a computationally feasible alternative to direct maximum likelihood estimates of phylogeny for mixed-model analyses of large, dynamically heterogenous data sets.

Rapid radiation events in the family Ursidae indicated by likelihood phylogenetic estimation from multiple fragments of mtDNA

The bear family (Ursidae) presents a number of phylogenetic ambiguities as the evolutionary relationships of the six youngest members (ursine bears) are largely unresolved. Recent mitochondrial DNA analyses have produced conflicting results with respect to the phylogeny of ursine bears. In an attempt to resolve these issues, we obtained 1916 nucleotides of mitochondrial DNA sequence data from six gene segments for all eight bear species and conducted maximum likelihood and maximum parsimony analyses on all fragments separately and combined. All six single-region gene trees gave different phylogenetic estimates; however, only for control region data was this significantly incongruent with the results from the combined data. The optimal phylogeny for the combined data set suggests that the giant panda is most basal followed by the spectacled bear. The sloth bear is the basal ursine bear, and there is weak support for a sister taxon relationship of the American and Asiatic black bears. The sun bear is sister taxon to the youngest clade containing brown bears and polar bears. Statistical analyses of alternate hypotheses revealed a lack of strong support for many of the relationships. We suggest that the difficulties surrounding the resolution of the evolutionary relationships of the Ursidae are linked to the existence of sequential rapid radiation events in bear evolution. Thus, unresolved branching orders during these time periods may represent an accurate representation of the evolutionary history of bear species.

Phylogeny, biogeography, and processes of molecular differentiation in Quercus subgenus Quercus (Fagaceae)

Quercus is one of the most abundant and economically important genera of woody plants in the Northern Hemisphere. To infer phylogenetic relationships within Quercus subgenus Quercus, chloroplast DNA (cpDNA) restriction sites and nucleotide sequences of the internal transcribed spacers (ITS) and the 5.8S coding region of the nuclear ribosomal DNA repeat were obtained for 44 individuals, including 25 species, intraspecific samples, and three outgroups. Separate parsimony analyses of each data set showed that individual gene trees were congruent and often complementary in supporting clades that generally corresponded to previously recognized taxonomic groups. Only one instance of strongly supported gene tree incongruence was detected and this anomalous pattern was explained best by ancient introgression of cpDNA across sectional boundaries. Simultaneous parsimony analysis of the pruned data sets supported the recognition of the strictly Eurasian section Cerris and resolved a novel hypothesis for the major infrageneric groups (Cerris- (Lobatae- (Protobalanus + Quercus sensu stricto))). The biogeographic hypothesis that all major oak lineages evolved locally at middle latitudes within the general distribution of their fossil ancestors was fully supported. This set of relationships also suggested a New World origin for the widespread white oaks of the Northern Hemisphere (section Quercus s. s.). For both data sets, inter- and intraspecific sampling within section Protobalanus showed little correspondence to morphological species. Greater cladistic structure among the samples was obtained by cpDNA restriction sites and two well-delimited plastomes types comprising a total of 15 distinct haplotypes were resolved. Haplotypes of 2 of the peripheral species in this species complex occupy terminal portions of one of the plastome clades, suggesting a more recent origin relative to those of more widespread species. The phylogeography of the two divergent plastome types suggested a north-south pattern, consistent with a Late Tertiary disjunction in the ancestral distribution of section Protobalanus.

The major opsin in bees (Insecta: Hymenoptera): A promising nuclear gene for higher level phylogenetics

We report the phylogenetic utility of the nuclear gene encoding the long-wavelength opsin (LW Rh) for tribes of bees. Aligned nucleotide sequences were examined in multiple taxa from the four tribes comprising the corbiculate bees within the subfamily Apinae. Phylogenetic analyses of sequence variation in a 502-bp fragment (approx 40% of the coding region) strongly supported the monophyly of each of the four tribes, which are well established from previous studies of morphology and DNA. Trees estimated from parsimony and maximum likelihood analyses of LW Rh sequences show a strongly supported relationship between the tribes Meliponini and Bombini, a relationship that has been found uniformly in studies of other genes (28S, 16S, and cytochrome b). All of the tribal clades as well as relationships among the tribes are supported by high bootstrap values, suggesting the utility of LW Rh in estimating tribal and subfamily rank for these bees. The sequences exhibit minimal base composition bias. Both 1st + 2nd and 3rd position sites provide information for estimating a reliable tree topology. These results suggest that LW Rh, which has not been reported previously in studies of organismal phylogenetics, could provide important new data from the nuclear genome for phylogeny reconstruction.

Homoplasy and adaptation in the atelid postcranium

Homoplasy is a ubiquitous phenomenon in phylogenetic investigations, but it is rarely investigated on its own. As a case study in the pattern and basis of homoplasy in primates, the atelid postcranium is discussed here. Characters available from Ford's ([1986] in Erwin J, Swindler DR, eds: Comparative Primate Biology I: Systematics, Evolution, and Anatomy (New York: Alan R. Liss), p 73-135; [1994] in Fleagle JG, Kay RF, eds: Anthropoid Origins (New York: Plenum Press), p 595-674) analyses of New World monkeys are mapped onto alternative phylogenetic trees for the family Atelidae to contrast patterns of character evolution and to develop explanatory hypotheses for differences in the trees. In an unrooted phylogenetic network, pitheciines do not group together because those pitheciines that routinely adopt hind limb suspensory postures (Chiropotes, Cacajao) share traits with atelines. Ford's (1986) work on phylogeny has shown that these traits are homoplastic and also identified potential synapomorphies of a clade comprised of modern pitheciins and atelines. However, following that work, congruence between studies of craniodental and molecular data suggested a still broader definition of atelids (including Callicebus and Cebupithecia), and in this case only one trait may define atelids, and several traits arise in parallel. The homoplastic characters in this phylogeny suggest that the phylogenetic signal in this set of postcranial data is overwhelmed by parallel adaptations to the use of climbing behaviors in all of Ford's atelids and suspensory postures in a more restricted set of taxa. These parallelisms probably indicate a bias of selective pressures in the South American environment, especially given the frequent, independent evolution of suspensory mammals there. This highlights the fact that homoplasy can be a dominant source of similarity in data partitions strongly influenced by a particular behavioral regime, in this case positional behavior.