Trees within trees: phylogeny and historical associations

The association between two or more lineages over evolutionary time is a recurrent theme spanning several different fields within biology, from molecular evolution to coevolution and biogeography. In each `historical association', one lineage is associated with another, and can be thought of as tracking the other over evolutionary time with a greater or lesser degree of fidelity. Examples include genes tracking organisms, parasites tracking hosts and organisms tracking geological and geographical changes. Parallels among these problems raise the tantalizing prospect that each is a special case of a more general problem, and that a single analytical tool can be applied to all three kinds of association.     

Treehopper trees: phylogeny of Membracidae (Hemiptera: Cicadomorpha: Membracoidea) based on molecules and morphology

Abstract. Recent independent phylogenetic analyses of membracid relationships based on molecular and morphological data have identified monophyletic lineages within the family. However, the results of these studies have not fully resolved treehopper phylogeny, and relationships among some higher membracid lineages remain in doubt. Portions of three datasets (958 aligned nucleotides from elongation factor‐1α, 2363 aligned nucleotides from 28S ribosomal DNA, and eighty‐three morphological features of adults and nymphs) introduced in recent studies were reanalysed separately and in combination with two new molecular datasets (321 aligned nucleotides from wingless and 1829 aligned nucleotides from 18S ribosomal DNA). The results of the combined data analyses, contrary to previous analyses of morphological data alone, grouped membracids into two well‐supported lineages, one comprising Stegaspidinae and Centrotinae, the other comprising Membracinae, Darninae and Smiliinae. The analyses recovered Centrotinae, Membracinae and Darninae as monophyletic groups, but Stegaspidinae was paraphyletic with respect to Centrotinae, and Smiliinae was polyphyletic with Micrutalini placed as a sister group to the clade comprising Membracinae, Darninae and Smiliinae. These results are consistent with the following hypotheses, proposed previously based on an analysis of morphological data: (1) the posterior pronotal process was derived and lost multiple times during the evolution of Membracidae; (2) Membracidae originated in the New World and reached the Old World subsequently via dispersal; (3) maternal care evolved independently multiple times and may or may not have been preceded by the acquisition of ant mutualism.     

Hidden Floridian biodiversity: mitochondrial and nuclear gene trees reveal four cryptic species within the scorched mussel, Brachidontes exustus, species complex

The well-documented Floridian 'Gulf/Atlantic' marine genetic disjunction provides an influential example of vicariant cladogenesis along a continental coastline for major elements of a diverse nearshore fauna. We are engaged in a two-part study that aims to place this disjunction into a regional Caribbean Basin phylogenetic perspective using the scorched mussel Brachidontes exustus as an exemplar. Our first step, documented here, is to thoroughly characterize the genetic structure of Floridian scorched mussel populations using mitochondrial (mt) and nuclear markers. Both sets of markers recovered the expected disjunction involving sister clades distributed on alternate flanks of peninsular Florida and lineage-specific mt molecular clocks placed its origin in the Pliocene. The two sister clades had distinct population genetic profiles and the Atlantic clade appears to have experienced an evolutionarily recent bottleneck, although plots of the relative estimates of N through time are consistent with its local persistence through the last Ice Age Maximum. Our primary novel result, however, was the discovery that the Gulf/Atlantic disjunction represents but one of three cryptic, nested genetic discontinuities represented in Floridian scorched mussel populations. The most pronounced phylogenetic split distinguished the Gulf and Atlantic sister clades from two additional nested cryptic sister clades present in samples taken from the southern Florida tropical marine zone. Floridian populations of B. exustus are composed of four cryptic taxa, a result consistent with the hypothesis that the Gulf/Atlantic disjunction in this morphospecies is but one of multiple latent regional genetic breakpoints.     

Gene trees, species trees, and morphology converge on a similar phylogeny of living gars (Actinopterygii: Holostei: Lepisosteidae), an ancient clade of ray-finned fishes

Extant gars represent the remaining members of a formerly diverse assemblage of ancient ray-finned fishes and have been the subject of multiple phylogenetic analyses using morphological data. Here, we present the first hypothesis of phylogenetic relationships among living gar species based on molecular data, through the examination of gene tree heterogeneity and coalescent species tree analyses of a portion of one mitochondrial (COI) and seven nuclear (ENC1, myh6, plagl2, S7 ribosomal protein intron 1, sreb2, tbr1, and zic1) genes. Individual gene trees displayed varying degrees of resolution with regards to species-level relationships, and the gene trees inferred from COI and the S7 intron were the only two that were completely resolved. Coalescent species tree analyses of nuclear genes resulted in a well-resolved and strongly supported phylogenetic tree of living gar species, for which Bayesian posterior node support was further improved by the inclusion of the mitochondrial gene. Species-level relationships among gars inferred from our molecular data set were highly congruent with previously published morphological phylogenies, with the exception of the placement of two species, Lepisosteus osseus and L. platostomus. Re-examination of the character coding used by previous authors provided partial resolution of this topological discordance, resulting in broad concordance in the phylogenies inferred from individual genes, the coalescent species tree analysis, and morphology. The completely resolved phylogeny inferred from the molecular data set with strong Bayesian posterior support at all nodes provided insights into the potential for introgressive hybridization and patterns of allopatric speciation in the evolutionary history of living gars, as well as a solid foundation for future examinations of functional diversification and evolutionary stasis in a "living fossil" lineage.     

Phytoseiidae (Acari: Mesostigmata) within citrus orchards in Florida: species distribution,relative and seasonal abundance within trees,associated vines and ground cover plants

Seven citrus orchards on reduced- to no-pesticide spray programs were sampled for predacious mites in the family Phytoseiidae (Acari: Mesostigmata) in central and south central Florida. Inner and outer canopy leaves, open flowers, fruit, twigs, and trunk scrapings were sampled monthly between September 1994 and January 1996. Vines and ground cover plants were sampled monthly between September 1994 and January 1996 in five of these orchards. The two remaining orchards were on full herbicide programs and ground cover plants were absent. Thirty-three species of phytoseiid mites were identified from 35,405 specimens collected within citrus tree canopies within the seven citrus orchards, and 8,779 specimens from vines and ground cover plants within five of the seven orchards. The six most abundant phytoseiid species found within citrus tree canopies were: Euseius mesembrinus (Dean) (20,948), Typhlodromalus peregrinus (Muma) (8,628), Iphiseiodes quadripilis (Banks) (2,632), Typhlodromips dentilis (De Leon) (592), Typhlodromina subtropica Muma and Denmark (519), and Galendromus helveolus (Chant) (315). The six most abundant species found on vines or ground cover plants were: T. peregrinus (6,608), E. mesembrinus (788), T. dentilis (451), I. quadripilis (203), T. subtropica (90), and Proprioseiopsis asetus (Chant) (48). The remaining phytoseiids included: Amblyseius aerialis (Muma), A. herbicolus (Chant), A. largoensis (Chant), A. multidentatus (Chant), A. sp. near multidentatus, A. obtusus (Koch), Chelaseius vicinus (Muma), Euseius hibisci Chant, Galendromus gratus (Chant), Metaseiulus mcgregori (Chant), Neoseiulus mumai (Denmark), N. vagus (Denmark), Phytoscutus sexpilis (Muma), Phytoseiulus macropilis (Banks), Proprioseiopsis detritus (Muma), P. dorsatus (Muma), P. macrosetae (Banks), P. rotundus (Muma), P. solens (De Leon), Typhlodromips deleoni (Muma), T. dillus (De Leon), T. dimidiatus (De Leon), T. mastus Denmark and Muma, T. simplicissimus (De Leon), and T. sp. near tunus, and Typhlodromus transvaalensis (Nesbitt). Eighty-two ground cover plants or vines were sampled within the five orchards and one or more phytoseiids were collected from 71 of these plants. Five ground cover plants with the highest numbers of phytoseiids included: Bidens alba (L.) DC (1,420 mites within 13 species), Solanum americanum L. (1,355 mites within 8 species), Amaranthus spinosus L. (1,137 mites within 11 species), Gnaphalium pensylvanicum Willd. (844 mites within 8 species) and Richardia brasiliensis (Meg.) Gomez (354 mites within 8 species).     

Extracting species trees from complex gene trees: reconciled trees and vertebrate phylogeny

Paralogy is a pervasive problem in trying to use nuclear gene sequences to infer species phylogenies. One strategy for dealing with this problem is to infer species phylogenies from gene trees using reconciled trees, rather than directly from the sequences themselves. In this approach, the optimal species tree is the tree that requires the fewest gene duplications to be invoked. Because reconciled trees can identify orthologous from paralogous sequences, there is no need to do this prior to the analysis. Multiple gene trees can be analyzed simultaneously; however, the problem of nonuniform gene sampling raises practical problems which are discussed. In this paper the technique is applied to phylogenies for nine vertebrate genes (aldolase, alpha-fetoprotein, lactate dehydrogenase, prolactin, rhodopsin, trypsinogen, tyrosinase, vassopressin, and Wnt-7). The resulting species tree shows much similarity with currently accepted vertebrate relationships.     

Eupalopsellidae and Stigmaeidae (Acari: Prostigmata) within citrus orchards in Florida: species distribution,relative and seasonal abundance within trees,associated vines,and ground cover plants

Seven citrus orchards on reduced- to no-pesticide spray programs were sampled for predacious mites in the families Eupalopsellidae and Stigmaeidae (Acari: Prostigmata) in central and south central Florida. Inner and outer canopy leaves, fruit, twigs, and trunk scrapings were sampled monthly between August 1994 and January 1996. Open flowers were sampled in March from five of the sites. Two species of eupalopsellid mites (Exothorhis caudata Summers and Saniosulus harteni (van-Dis and Ueckermann)) were identified from 252 specimens collected within citrus tree canopies within the seven citrus orchards of which 249 were E. caudata. Only two E. caudata were collected from ground cover plants within five of the seven orchards. Eight species of Stigmaeidae were identified from 5,637 specimens: Agistemus floridanus Gonzalez, A. terminalis Gonzalez, Eustigmaeus arcuata (Chandhri), E. sp. near arcuata, E. segnis (Koch), Mediostigmaeus citri (Rakha and McCoy), Stigmaeus seminudus Wood, and Zetzellia languida Gonzalez were collected from within citrus tree canopies from seven orchard sites. Agistemus floridanus was the only species in either family that was abundant with 5,483 collected from within citrus tree canopies compared with only 39 from vine or ground cover plants. A total of 431 samples from one or more of 82 vines and ground cover plants were sampled monthly between September 1994 and January 1996 in five of these orchards and one or more eupalopsellids or stigmaeids were collected from 19 of these plants. Richardia brasiliensis (Meg.) Gomez had nine A. floridanus from 5 of 25 samples collected from this plant. Solanum sp. had five A. floridanus from three samples taken. Both eupalopsellid and stigmaeid species numbers represented <1 % of the total numbers of phytoseiid species taken from the same plants. The two remaining orchards were on full herbicide programs and ground cover plants were absent. Agistemus floridanus was more abundant in the citrus orchards with on-going or recent herbicide programs compared with orchards having well-developed ground cover plants. Agistemus floridanus was most abundant on inner leaves between January and April and again during September through November. Additional collection records of E. caudata, S. harteni, A. terminalis, M. citri, Z. languida, and Zetzellia sp. near silvicola within Florida citrus orchards between 1989 and 2004 are included. Four species of Eupalopsellidae and ten species of Stigmaeidae occur within Florida citrus orchards.     

Relationships between gene trees and species trees

It is well known that a phylogenetic tree (gene tree) constructed from DNA sequences for a genetic locus does not necessarily agree with the tree that represents the actual evolutionary pathway of the species involved (species tree). One of the important factors that cause this difference is genetic polymorphism in the ancestral species. Under the assumption of neutral mutations, this problem can be studied by evaluating the probability (P) that a gene tree has the same topology as that of the species tree. When one gene (allele) is used from each of the species involved, the probability can be expressed as a simple function of Ti = ti/(2N), where ti is the evolutionary time measured in generations for the ith internodal branch of the species tree and N is the effective population size. When any of the Ti's is less than 1, the probability P becomes considerably less than 1.0. This probability cannot be substantially increased by increasing the number of alleles sampled from a locus. To increase the probability, one has to use DNA sequences from many different loci that have evolved independently of each other.      

On the length distribution of external branches in coalescence trees: genetic diversity within species

Let Z(n) denote the length of an external branch, chosen at random from a Kingman n-coalescent. Based on a recursion for the distribution of Z(n), we show that nZ(n) converges in distribution, as n tends to infinity, to a non-negative random variable Z with density x--> 8/(2+x)(3), x>or=0. This result facilitates the study of the time to the most recent common ancestor of a randomly chosen individual and its closest relative in a given population. This time span also reflects the maximum relatedness between a single individual and the rest of the population. Therefore, it measures the uniqueness of a random individual, a central characteristic of the genetic diversity of a population.     

Alexandrium diversaporum sp. nov., a new non-saxitoxin producing species: Phylogeny,morphology and sxtA genes

Species of the PST producing planktonic marine dinoflagellate genus Alexandrium have been intensively scrutinised, and it is therefore surprising that new taxa can still be found. Here we report a new species, Alexandrium diversaporum nov. sp., isolated from spherical cysts found at two sites in Tasmania, Australia. This species differs in its morphology from all previously reported Alexandrium species, possessing a unique combination of morphological features: the presence of 2 size classes of thecal pores on the cell surface, a medium cell size, the size and shape of the 6″, 1′, 2⁗ and Sp plates, the lack of a ventral pore, a lack of anterior and posterior connecting pores, and a lack of chain formation. We determined the relationship of the two strains to other species of Alexandrium based on an alignment of concatenated SSU-ITS1, 5.8S, ITS2 and partial LSU ribosomal RNA sequences, and found A. diversaporum to be a sister group to Alexandrium leei with high support. A. leei shares several morphological features, including the relative size and shapes of the 6″, 1′, 2⁗ and Sp plates and the fact that some strains of A. leei have two size classes of thecal pores. We examined A. diversaporum strains for saxitoxin production and found them to be non-toxic. The species lacked sequences for the domain A4 of sxtA, as has been previously found for non-saxitoxin producing species of Alexandrium.     

Deadly combination of genes and drought: increased mortality of herbivore-resistant trees in a foundation species

Current climate models predict a shift to warmer, drier conditions in the southwestern US. While major shifts in plant distribution are expected to follow these climate changes, interactions among species and intraspecific genetic variation rarely have been incorporated into models of future plant distributions. We examined the drought‐related mortality of pinyon pine (Pinus edulis) in northern Arizona focusing on trees that showed genetically‐based resistance or susceptibility to a nonlethal herbivore, the shoot‐boring moth, Dioryctria albovittella. Because moth resistant trees have outperformed susceptible trees during 20 years of study, and herbivory has been shown to increase drought related mortality, we expected higher mortality rates in susceptible trees. However, our field observations and greenhouse experiments showed several unexpected patterns relevant to understanding the consequences of climate change: (1) The mortality of adult P. edulis resistant to the moth was three times higher than the mortality of trees susceptible to the moth. (2) Over a few years, differential mortality caused a shift in stand structure from resistant dominated to equality (3 : 1 resistant : susceptible to 1 : 1). (3) Adult moth resistant trees suffered significantly greater water stress than adult moth susceptible trees, suggesting that variation among the two groups in drought tolerance may be a mechanism for differential mortality. (4) When grown under drought conditions in the greenhouse, seedlings from resistant mothers died sooner than seedlings from susceptible mothers. These data support the hypothesis that drought can act as an agent of balancing selection and that drought resistance is a heritable trait. Taken together, our findings suggest that genetic variation in a population can be an important factor in determining its response to future climate change, and argue for the inclusion of genetics into models developed to understand the consequences of climate change.     

Speciation by postzygotic isolation: forces, genes and molecules

New species arise as reproductive isolation evolves between diverging populations. Here we review recent work in the genetics of postzygotic reproductive isolation-the sterility and inviability of species hybrids. Over the last few years, research has taken two new directions. First, we have begun to learn a good deal about the population genetic forces driving the evolution of postzygotic isolation. It has, for instance, become increasingly clear that conflict-driven processes, like sexual selection and meiotic drive, may contribute to the evolution of hybrid sterility. Second, we have begun to learn something about the identity and molecular characteristics of the actual genes causing hybrid problems. Although molecular genetic data are limited, early findings suggest that "speciation genes" correspond to loci having normal functions within species and that these loci sometimes diverge as a consequence of evolution in gene regulation.     

Total evidence: molecules, morphology, and the phylogenetics of cichlid fishes

We present a most comprehensive phylogenetic analysis of the family Cichlidae. New data analyzed include mitochondrial 16S rRNA sequences and two nuclear loci (Tmo-M27 and Tmo-4C4) for a large taxonomic sampling with emphasis on South American species. We also incorporate a published morphological data set for a total evidence analysis. Character congruence among mitochondrial (74 taxa) and nuclear data (50 taxa) was high. However, partition-homogeneity tests suggest significant heterogeneity among molecular and morphological data. In agreement with results obtained from molecular data alone, total evidence analysis (1,460 characters for 34 taxa) supports a robust phylogenetic hypothesis for the family Cichlidae that is congruent with drift-vicariance events associated with the fragmentation of Gondwana. Our analyses confirm the placement of Malagasy/Indian cichlids as the most basal lineages, with a sister-group relationship to the monophyletic African and Neotropical clades. Total evidence suggests that the controversial African genus Heterochromis is at the base of the African radiation. Among more than 50 Neotropical genera analyzed, Retroculus is identified as the basal taxon, with successive branching of Cichla, Astronotus, geophagines (including crenicichlines) + chaetobranchines, and cichlasomines + heroines. Relative rate tests applied to mitochondrial DNA suggest significantly higher rates of genetic variation in Neotropical than in African taxa, and both mitochondrial and nuclear sequences show that rate heterogeneity among Neotropical lineages is confined to the geophagine cichlids.     

TREEasy: An automated workflow to infer gene trees,species trees,and phylogenetic networks from multilocus data

Multilocus genomic data sets can be used to infer a rich set of information about the evolutionary history of a lineage, including gene trees, species trees, and phylogenetic networks. However, user‐friendly tools to run such integrated analyses are lacking, and workflows often require tedious reformatting and handling time to shepherd data through a series of individual programs. Here, we present a tool written in Python—TREEasy—that performs automated sequence alignment (with MAFFT), gene tree inference (with IQ‐Tree), species inference from concatenated data (with IQ‐Tree and RaxML‐NG), species tree inference from gene trees (with ASTRAL, MP‐EST, and STELLS2), and phylogenetic network inference (with SNaQ and PhyloNet). The tool only requires FASTA files and nine parameters as inputs. The tool can be run as command line or through a Graphical User Interface (GUI). As examples, we reproduced a recent analysis of staghorn coral evolution, and performed a new analysis on the evolution of the “WGD clade” of yeast. The latter revealed novel patterns that were not identified by previous analyses. TREEasy represents a reliable and simple tool to accelerate research in systematic biology ( https://github.com/MaoYafei/TREEasy ).     

Gene trees and species trees are not the same

The relationship between species is usually represented as a bifurcating tree with the branching points representing speciation events. The ancestry of genes taken from these species can also be represented as a tree, with the branching points representing ancestral genes. The time back to the branching points, and even the branching order, can be different between the two trees. This possibility is widely recognized, but the discrepancies are often thought to be small. A different picture is emerging from new empirical evidence, particularly that based on multiple loci or on surveys with a wide geographical scope. The discrepancies must be taken into account when estimating the timing of speciation events, especially the more recent branches. On the positive side, the different timings at different loci provide information about the ancestral populations.     

Coalescent histories for discordant gene trees and species trees

Given a gene tree and a species tree, a coalescent history is a list of the branches of the species tree on which coalescences in the gene tree take place. Each pair consisting of a gene tree topology and a species tree topology has some number of possible coalescent histories. Here we show that, for each n≥7, there exist a species tree topology S and a gene tree topology G≠S, both with n leaves, for which the number of coalescent histories exceeds the corresponding number of coalescent histories when the species tree topology is S and the gene tree topology is also S. This result has the interpretation that the gene tree topology G discordant with the species tree topology S can be produced by the evolutionary process in more ways than can the gene tree topology that matches the species tree topology, providing further insight into the surprising combinatorial properties of gene trees that arise from their joint consideration with species trees.