Does gene flow destroy phylogenetic signal? The performance of three methods for estimating species phylogenies in the presence of gene flow

Incomplete lineage sorting has been documented across a diverse set of taxa ranging from song birds to conifers. Such patterns are expected theoretically for species characterized by certain life history characteristics (e.g. long generation times) and those influenced by certain historical demographic events (e.g. recent divergences). A number of methods to estimate the underlying species phylogeny from a set of gene trees have been proposed and shown to be effective when incomplete lineage sorting has occurred. The further effects of gene flow on those methods, however, remain to be investigated. Here, we focus on the performance of three methods of species tree inference, ESP-COAL, minimizing deep coalescence (MDC), and concatenation, when incomplete lineage sorting and gene flow jointly confound the relationship between gene and species trees. Performance was investigated using Monte Carlo coalescent simulations under four models (n-island, stepping stone, parapatric, and allopatric) and three magnitudes of gene flow (N_em = 0.01, 0.10, 1.00). Although results varied by the model and magnitude of gene flow, methods incorporating aspects of the coalescent process (ESP-COAL and MDC) performed well, with probabilities of identifying the correct species tree topology typically increasing to greater than 0.75 when five more loci are sampled. The only exceptions to that pattern included gene flow at moderate to high magnitudes under the n-island and stepping stone models. Concatenation performs poorly relative to the other methods. We extend these results to a discussion of the importance of species and population phylogenies to the fields of molecular systematics and phylogeography using an empirical example from Rhododendron.     

Inferring speciation rates from phylogenies

Abstract It is possible to estimate the rate of diversification of clades from phylogenies with a temporal dimension. First, I present several methods for constructing confidence intervals for the speciation rate under the simple assumption of a pure birth process. I discuss the relationships among these methods in the hope of clarifying some fundamental theory in this area. Their performances are compared in a simulation study and one is recommended for use as a result. A variety of other questions that may, in fact, be the questions of primary interest (e.g., Has the rate of cladogenesis been declining?) are then recast as biological variants of the purely statistical question—Is the birth process model appropriate for my data? Seen in this way, a preexisting arsenal of statistical techniques is opened up for use in this area: in particular, techniques developed for the analysis of Poisson processes and the analysis of survival data. These two approaches start from different representations of the data—the branch lengths in the tree—and I explicitly relate the two. Aiming for a synoptic account of useful theory in this area, I briefly discuss some important results from the analysis of two distinct birth‐death processes: the one introduced into this area by Hey (1992) is refitted with some powerful statistical tools.     

Efficiency of the Neighbor-Joining Method in Reconstructing Deep and Shallow Evolutionary Relationships in Large Phylogenies

The neighbor-joining (NJ) method is widely used in reconstructing large phylogenies because of its computational speed and the high accuracy in phylogenetic inference as revealed in computer simulation studies. However, most computer simulation studies have quantified the overall performance of the NJ method in terms of the percentage of branches inferred correctly or the percentage of replications in which the correct tree is recovered. We have examined other aspects of its performance, such as the relative efficiency in correctly reconstructing shallow (close to the external branches of the tree) and deep branches in large phylogenies; the contribution of zero-length branches to topological errors in the inferred trees; and the influence of increasing the tree size (number of sequences), evolutionary rate, and sequence length on the efficiency of the NJ method. Results show that the correct reconstruction of deep branches is no more difficult than that of shallower branches. The presence of zero-length branches in realized trees contributes significantly to the overall error observed in the NJ tree, especially in large phylogenies or slowly evolving genes. Furthermore, the tree size does not influence the efficiency of NJ in reconstructing shallow and deep branches in our simulation study, in which the evolutionary process is assumed to be homogeneous in all lineages. Received: 7 March 2000 / Accepted: 2 August 2000     

Phylogeography and history of giant Galápagos tortoises

Abstract.— We examined the phylogeography and history of giant Galàpagos tortoise populations based on mito-chondrial DNA sequence data from 161 individuals from 21 sampling sites representing the 11 currently recognized extant taxa. Molecular clock and geological considerations indicate a founding of the monophyletic Galàpagos lineage around 2–3 million years ago, which would allow for all the diversification to have occurred on extant islands. Founding events generally occurred from geologically older to younger islands with some islands colonized more than once. Six of the 11 named taxa can be associated with monophyletic maternal lineages. One, Geochelone porteri on Santa Cruz Island, consists of two distinct populations connected by the deepest node in the archipelago-wide phylogeny, whereas tortoises in northwest Santa Cruz are closely related to those on adjacent Pinzón Island. Volcan Wolf, the northernmost volcano of Isabela Island, consists of both a unique set of maternal lineages and recent migrants from other islands, indicating multiple colonizations possibly due to human transport or multiple colonization and partial elimination through competition. These genetic findings are consistent with the mixed morphology of tortoises on this volcano. No clear genetic differentiation between two taxa on the two southernmost volcanoes of Isabela was evident. Extinction of crucial populations by human activities confounds whether domed versus saddleback carapaces of different populations are mono- or polyphyletic. Our findings revealed a complex phylogeography and history for this tortoise radiation within an insular environment and have implications for efforts to conserve these endangered biological treasures.     

PATTERNS IN TREE BALANCE AMONG CLADISTIC,PHENETIC, AND RANDOMLY GENERATED PHYLOGENETIC TREES

I examine patterns in tree balance for a sample of 208 cladograms and phenograms from the recent literature. I provide an expression for expected imbalance under a simple, uniform-rate random speciation model, and I estimate variances by simulation for the same model. Imbalance decreases with tree size (number of included taxa) in both theoretical and literature trees. In contrast to previous suggestions, I find cladistic trees to be no more imbalanced than phenetic trees when confounding variables are appropriately controlled. The degree of imbalance found in literature trees is inconsistent with the uniform-rate speciation model; this is most likely a result of variability in speciation and extinction rates among real lineages. The existence of such variation is a necessary (but not sufficient) condition for the operation of the macroevolutionary processes of species sorting and species selection.     

Undirectional interspecific mating in Tribolium castaneum and T. confusum: evolutionary and ecological implications

Interspecific mating between two species of Tribolium occurs only between males of T. confusum and females of T. castaneum. The reciprocal mating combination was not observed. This pattern of unidirectional mating resulted in a frequency-independent reduction in the number of inseminated females in mixed populations in comparison with single-species mating groups. The ecological significance in terms of interspecific competition, and the possibility of identifying evolutionarily ancestral and derived species from such data are discussed.

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Accouplements non réciproques entre Tribolium castaneum et T. confusum: conséquences évolutives et écologiques

Résumé Les accouplements interspécifiques entre deux espèces de Tribolium n'ont lieu qu'entre mâles de T. confusum et femelles de T. castaneum. Les combinaisons réciproques n'ont pas été observées. Ce type d'accouplement asymétrique a provoqué une réduction indépendante de la fréquence dans le nombre de femelles inséminées dans les populations par rapport aux groupes d'accouplements monospécifiques. La discussion porte sur la signification écologique dans la compétition interspécifique et les possibilités d'identification des espèces ancestrales et dérivées.

     

THE MACROEVOLUTIONARY CONSEQUENCES OF ECOLOGICAL DIFFERENCES AMONG SPECIES

Abstract:  In this paper, I examine the dynamics of species richness in a model system in which multiple species compete in a metacommunity (multiple patches linked by dispersal). Patches lie along an environmental gradient, and new species are introduced into the system by speciation of existing species. This model is used to explore how the ecological similarity of species influences the patterns in community structure that result and to determine whether patterns in fossil and systematics data may be signatures for different types of community structure. Making species more similar overall along the entire gradient or making new species that have more similar optimal positions along the gradient to their progenitor both increase the time required to drive species extinction. As a result, making species more similar ecologically to one another increases overall species richness because of an increased frequency of transient species in the system. Having more transient species in systems shifted the longevity distributions of species in the fossil record towards having a greater frequency of shorter duration species, and the age distribution of extant species that would be estimated from molecular phylogenies also had a higher frequency of younger aged species. Comparisons of these results with species longevity distributions extracted from two data sets and with species ages derived from species-level molecular phylogenies strongly suggest that transient species are an important component of real biological communities.     

The biogeography of the austral, subalpine genus Ourisia (Plantaginaceae) based on molecular phylogenetic evidence: South American origin and dispersal to New Zealand and Tasmania

Molecular phylogenetic analyses of 26 of the 28 species of Ourisia , including eight of ten subspecies and two purported natural hybrids, are presented and used to examine the biogeography of the genus, which is distributed in subalpine to alpine habitats of South America, New Zealand and Tasmania. Gondwanan vicariance, often cited as the cause of this classic austral biogeographical pattern, was rejected by parametric bootstrapping of our combined dataset. Alternatively, various lines of evidence are presented in favour of a South American origin of Ourisia and subsequent dispersal to Australasia. Specifically, the genus likely arose in the Andes of central Chile and spread to southern Chile and Argentina, to the north-central Andes, and finally to Tasmania and New Zealand. The ancestor of the New Zealand species probably first arrived on the South Island, where the New Zealand species of Ourisia are most diverse, and migrated to the North and Stewart Islands. Because the Tasmanian and New Zealand species are sister to one another, the direction of dispersal between these two areas is equivocal. These results agree with other molecular phylogenetic studies that show that past dispersal between southern hemisphere continents has played an important role in the evolutionary history of many high-elevation austral plants. Our data also show that within South America, many of the geographical barriers (with the exception of the Atacama Desert) that have played a role in the evolution of other plant groups have not affected Ourisia species. Within New Zealand, the phylogeny and biogeography of species of Ourisia coincide with the geological history of the country and patterns of other alpine plants. © 2006 The Linnean Society of London, Biological Journal of the Linnean Society , 2006, 87 , 479–513.     

得与失:苦苣苔科新的属级界定与分类系统——中国该科植物之变迁(英文)

过去20年对苦苣苔科植物的分子系统学研究已经极大地拓展了对这个科的种间关系与属一级之界定的理解。该文提供了一个苦苣苔科植物新分类系统,与传统的经典形态学分类系统比较,这一新系统被认为能更好地反映科下分类单元彼此之间的自然关系。众多传统意义上的属被分割、合并或者重新定义,这些巨大的分类变动正在影响着中国的苦苣苔科植物系统分类。此外,基于最近采集的材料,一些新属得以建立,一方面说明在中国还有相当多的野外工作需要做;而另一方面则再次证明了中国的苦苣苔科植物多样性是如此之丰富。在此,针对目前已经完成的工作和分类结论,对中国苦苣苔科植物的新分类系统进行了总结与概述,并深入地讨论了部分传统分类学上存在困惑的疑难属。