autoinfer1.0: a computer program to infer biogeographical events automatically

autoinfer is a computer program for biogeographical inference based on nested clade analysis. To reduce the obscurity caused by manual inference, we defined geographically concordant clades and intermediate geographical areas between two clades. The program will perform most of the inferences automatically with a minimum of input from the user. We believe that autoinfer will save much time for the user compared with using the inference key by hand and, furthermore, will reduce the errors of inference resulting from different criteria in deduction.     

Population genetics, phylogeography and speciation of Cystodytes (Ascidiacea) in the western Mediterranean Sea

Several morphotypes that so far have been attributed to the allegedly cosmopolitan ascidian Cystodytes dellechiajei occur in the Mediterranean Sea. Colour variation is the difference most frequently reported. In this study, we addressed the genetic structure of this ascidian in relation to geographical location and colour morph. Partial sequences of the gene cytochrome  c oxidase subunit 1 (COI) were obtained from seven populations of the western Mediterranean, encompassing eight colour varieties. All population genetic analyses (exact test, pairwise F _ST, hierarchical analysis of molecular variance, multidimensional scaling, nested clade analysis) indicated clearly that differences between colour morphs are large enough to obscure any geographical differentiation when colours are combined within localities. When variance due to colour divergence was removed, however, a significant geographical variability between localities remained. The genetic divergence between the colour morphs analysed was significant in comparisons of the brown and purple forms with the others, but not among the green, blue, and white morphs. Phylogeographic analyses suggest that population fragmentation and range expansions have shaped the present-day distribution of the haplotypes. Taken together with existing chemotype information, our results indicate that several species are present in the area, and that a thorough revision of the genus is necessary.  © 2006 The Linnean Society of London, Biological Journal of the Linnean Society , 2006, 88 , 203–214.     

Statistical hypothesis testing in intraspecific phylogeography: nested clade phylogeographical analysis vs. approximate Bayesian computation

Nested clade phylogeographical analysis (NCPA) and approximate Bayesian computation (ABC) have been used to test phylogeographical hypotheses. Multilocus NCPA tests null hypotheses, whereas ABC discriminates among a finite set of alternatives. The interpretive criteria of NCPA are explicit and allow complex models to be built from simple components. The interpretive criteria of ABC are ad hoc and require the specification of a complete phylogeographical model. The conclusions from ABC are often influenced by implicit assumptions arising from the many parameters needed to specify a complex model. These complex models confound many assumptions so that biological interpretations are difficult. Sampling error is accounted for in NCPA, but ABC ignores important sources of sampling error that creates pseudo-statistical power. NCPA generates the full sampling distribution of its statistics, but ABC only yields local probabilities, which in turn make it impossible to distinguish between a good fitting model, a non-informative model, and an over-determined model. Both NCPA and ABC use approximations, but convergences of the approximations used in NCPA are well defined whereas those in ABC are not. NCPA can analyse a large number of locations, but ABC cannot. Finally, the dimensionality of tested hypothesis is known in NCPA, but not for ABC. As a consequence, the 'probabilities' generated by ABC are not true probabilities and are statistically non-interpretable. Accordingly, ABC should not be used for hypothesis testing, but simulation approaches are valuable when used in conjunction with NCPA or other methods that do not rely on highly parameterized models.     

Phylogeographical patterns in chloroplast DNA variation within the Acacia acuminata (Leguminosae: Mimosoideae) complex in Western Australia

Abstract The Acacia acuminata complex includes three taxa, A. acuminata ssp. acuminata, A. acuminata ssp. burkittii and A. oldfieldii, along with several informal variants of A. acuminata. It is widespread throughout southern Australia with the centre of diversity in south‐west Western Australia. Phylogeographical patterns in the complex were investigated using a nested clade analysis of cpDNA RFLPs from 25 populations in Western Australia. Except for A. oldfieldii that was clearly identified as a distinct entity, haplotypes were not restricted to sub‐specific taxa or variants within A. acuminata. There was significant association between phylogenetic position of many haplotypes and their geographical distribution. The fine‐scale phylogeographical patterns were complex but at deeper levels in the phylogeny there was evidence of divergence between two lineages. The pattern of shared haplotypes between lineages suggests retention of ancestral polymorphism as a result of incomplete lineage sorting. The divergence of these lineages is consistent with fragmentation caused by climatic instability during the Pleistocene.     

Beringian origins and cryptic speciation events in the fly agaric (Amanita muscaria)

Amanita muscaria sensu lato has a wide geographic distribution, occurring in Europe, Asia, Africa, Australia, New Zealand, and North, Central and South America. Previous phylogenetic work by others indicates three geographic clades (i.e. 'Eurasian', 'Eurasian-alpine' and 'North American' groups) within A. muscaria. However, the historical dispersal patterns of A. muscaria remained unclear. In our project, we collected specimens from arctic, boreal and humid temperate regions in Alaska, and generated DNA sequence data from the protein-coding beta-tubulin gene and the internal transcribed spacer (ITS) and large subunit (LSU) regions of the ribosomal DNA repeat. Homologous sequences from additional A. muscaria isolates were downloaded from GenBank. We conducted phylogenetic and nested clade analyses (NCA) to reveal the phylogeographic history of the species complex. Although phylogenetic analyses confirmed the existence of the three above-mentioned clades, representatives of all three groups were found to occur sympatrically in Alaska, suggesting that they represent cryptic phylogenetic species with partially overlapping geographic distributions rather than being allopatric populations. All phylogenetic species share at least two morphological varieties with other species, suggesting ancestral polymorphism in pileus and wart colour pre-dating their speciations. The ancestral population of A. muscaria likely evolved in the Siberian-Beringian region and underwent fragmentation as inferred from NCA and the coalescent analyses. The data suggest that these populations later evolved into species, expanded their range in North America and Eurasia. In addition to range expansions, populations of all three species remained in Beringia and adapted to the cooling climate.     

WHY DOES A METHOD THAT FAILS CONTINUE TO BE USED?

As a critical framework for addressing a diversity of evolutionary and ecological questions, any method that provides accurate and detailed phylogeographic inference would be embraced. What is difficult to understand is the continued use of a method that not only fails, but also has never been shown to work--nested clade analysis is applied widely even though the conditions under which the method will provide reliable results have not yet been demonstrated. This contradiction between performance and popularity is even more perplexing given the recent methodological and computational advances for making historical inferences, which include estimating population genetic parameters and testing different biogeographic scenarios. Here I briefly review the history of criticisms and rebuttals that focus specifically on the high rate of incorrect phylogeographic inference of nested-clade analysis, with the goal of understanding what drives its unfettered popularity. In this case, the appeal of what nested-clade analysis claims to do--not what the method actually achieves--appears to explain its paradoxical status as a favorite method that fails. What a method promises, as opposed to how it performs, must be considered separately when evaluating whether the method represents a valuable tool for historical inference.     

Population structure between environmentally transmitted vibrios and bobtail squids using nested clade analysis

Squids from the genus Euprymna (Cephalopoda: Sepiolidae) and their symbiotic bacteria Vibrio fischeri form a mutualism in which vibrios inhabit a complex light organ within the squid host. A host-mediated daily expulsion event seeds surrounding seawater with symbiotically capable V. fischeri that environmentally colonize newly hatched axenic Euprymna juveniles. Competition experiments using native and non-native Vibrio have shown that this expulsion/re-colonization phenomenon has led to cospeciation in this system in the Pacific Ocean; however, the genetic architecture of these symbiotic populations has not been determined. Using genetic diversity and nested clade analyses we have examined the variation and history of three allopatric Euprymna squid species (E. scolopes of Hawaii, E. hyllebergi of Thailand, and E. tasmanica from Australia) and their respective Vibrio symbionts. Euprymna populations appear to be very genetically distinct from each other, exhibiting little or no migration over large geographical distances. In contrast, Vibrio symbiont populations contain more diverse haplotypes, suggesting both host presence and unidentified factors facilitating long-distance migration structure in Pacific Vibrio populations. Findings from this study highlight the importance of how interactions between symbiotic organisms can unexpectedly shape population structure in phylogeographical studies.