TCS: a computer program to estimate gene genealogies.
About: This article is published in Molecular Ecology.The article was published on 2000-10-01. It has received 9118 citations till now.
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TL;DR: Popart is presented, an integrated software package that provides a comprehensive implementation of haplotype network methods, phylogeographic visualisation tools and standard statistical tests, together with publication‐ready figure production.
Abstract: Summary
Haplotype networks are an intuitive method for visualising relationships between individual genotypes at the population level.
Here, we present popart, an integrated software package that provides a comprehensive implementation of haplotype network methods, phylogeographic visualisation tools and standard statistical tests, together with publication-ready figure production.
popart also provides a platform for the implementation and distribution of new network-based methods – we describe one such new method, integer neighbour-joining.
The software is open source and freely available for all major operating systems.
3,634 citations
TL;DR: In this paper, the authors use mitochondrial DNA variation to delimit species in a poorly known beetle radiation in the genus Rivacindela from arid Australia, using a new likelihood method that determines the point of transition from species-level (speciation and extinction) to population-level evolutionary processes.
Abstract: Cataloging the very large number of undescribed species of insects could be greatly accelerated by automated DNA based approaches, but procedures for large-scale species discovery from sequence data are currently lacking. Here, we use mitochondrial DNA variation to delimit species in a poorly known beetle radiation in the genus Rivacindela from arid Australia. Among 468 individuals sampled from 65 sites and multiple morphologically distinguishable types, sequence variation in three mtDNA genes (cytochrome oxidase subunit 1, cytochrome b, 16S ribosomal RNA) was strongly partitioned between 46 or 47 putative species identified with quantitative methods of species recognition based on fixed unique ("diagnostic") characters. The boundaries between groups were also recognizable from a striking increase in branching rate in clock-constrained calibrated trees. Models of stochastic lineage growth (Yule models) were combined with coalescence theory to develop a new likelihood method that determines the point of transition from species-level (speciation and extinction) to population-level (coalescence) evolutionary processes. Fitting the location of the switches from speciation to coalescent nodes on the ultrametric tree of Rivacindela produced a transition in branching rate occurring at 0.43 Mya, leading to an estimate of 48 putative species (confidence interval for the threshold ranging from 47 to 51 clusters within 2 logL units). Entities delimited in this way exhibited biological properties of traditionally defined species, showing coherence of geographic ranges, broad congruence with morphologically recognized species, and levels of sequence divergence typical for closely related species of insects. The finding of discontinuous evolutionary groupings that are readily apparent in patterns of sequence variation permits largely automated species delineation from DNA surveys of local communities as a scaffold for taxonomy in this poorly known insect group.
2,020 citations
TL;DR: Whereas traditional phylogenetic methods assume bifurcating trees, several networking approaches have recently been developed to estimate intraspecific genealogies that take into account population-level phenomena.
Abstract: Intraspecific gene evolution cannot always be represented by a bifurcating tree. Rather, population genealogies are often multifurcated, descendant genes coexist with persistent ancestors and recombination events produce reticulate relationships. Whereas traditional phylogenetic methods assume bifurcating trees, several networking approaches have recently been developed to estimate intraspecific genealogies that take into account these population-level phenomena.
1,495 citations
TL;DR: It is shown that one key to invasion success may be the occurrence of multiple introductions that transform among- population variation in native ranges to within-population variation in introduced areas.
Abstract: A genetic paradox1,2 exists in invasion biology: how do introduced populations, whose genetic variation has probably been depleted by population bottlenecks, persist and adapt to new conditions? Lessons from conservation genetics show that reduced genetic variation due to genetic drift and founder effects limits the ability of a population to adapt, and small population size increases the risk of extinction1,3,4. Nonetheless, many introduced species experiencing these same conditions during initial introductions persist, expand their ranges, evolve rapidly and become invasive. To address this issue, we studied the brown anole, a worldwide invasive lizard. Genetic analyses indicate that at least eight introductions have occurred in Florida from across this lizard's native range, blending genetic variation from different geographic source populations and producing populations that contain substantially more, not less, genetic variation than native populations. Moreover, recently introduced brown anole populations around the world originate from Florida, and some have maintained these elevated levels of genetic variation. Here we show that one key to invasion success may be the occurrence of multiple introductions that transform among-population variation in native ranges to within-population variation in introduced areas. Furthermore, these genetically variable populations may be particularly potent sources for introductions elsewhere. The growing problem of invasive species introductions brings considerable economic and biological costs5,6. If these costs are to be mitigated, a greater understanding of the causes, progression and consequences of biological invasions is needed7.
1,014 citations
01 Jan 2002
TL;DR: Results indicate that an introduction of a non-native strain of Phragmites has occurred, and the introduced type has displaced native types as well as expanded to regions previously not known to have PhragMites.
Abstract: iological invasions threaten species and ecosystems world-wide (1). An estimated 50,000 exotic species have beenintroduced to the United States, of which 5,000 are plant speciesthat have escaped and now exist in natural environments (2).Both the actual number of invaders and the impacts of thesespecies may be underestimated because of the presence ofcryptic invaders, or species that cannot be easily classified asnative or introduced (3). Over the past decade, use of PCR-basedmolecular techniques have revealed repeated occurrences ofsuch invasions in marine ecosystems (4–6), and studies havedemonstrated both genetic and physiological differences be-tween invading and native populations (6). Given that crypticinvaders typically are unrecognized or are mistaken for nativespecies, knowledge of historical trends in geographic distributionand population genetic structure in cases of suspected introduc-tions are of particular interest when trying to reconstruct theinvasionhistoryofaspecies.Insuchcases,museumorherbariumspecimens are an invaluable resource for reconstructing popu-lation history.Common reed,
942 citations
References
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TL;DR: The combination of these phylogenies with powerful new statistical approaches for the analysis of biological evolution is challenging widely held beliefs about the history and evolution of life on Earth.
Abstract: Phylogenetic trees describe the pattern of descent amongst a group of species. With the rapid accumulation of DNA sequence data, more and more phylogenies are being constructed based upon sequence comparisons. The combination of these phylogenies with powerful new statistical approaches for the analysis of biological evolution is challenging widely held beliefs about the history and evolution of life on Earth.
4,159 citations
"TCS: a computer program to estimate..." refers background in this paper
...In a recent review, Pagel (1999) eloquently outline a number of uses for phylogenetic information from discovery of drug resistance to reconstructing the common ancestor to all of life....
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TL;DR: A strategy for estimating the set of cladograms that are consistent with a particular sample of either restriction site or nucleotide sequence data and that includes the possibility of recombination is presented.
Abstract: We previously developed a cladistic approach to identify subsets of haplotypes defined by restriction endonuclease mapping or DNA sequencing that are associated with significant phenotypic deviations. Our approach was limited to segments of DNA in which little recombination occurs. In such cases, a cladogram can be constructed from the restriction site or sequence data that represents the evolutionary steps that interrelate the observed haplotypes. The cladogram is used to define a nested statistical design to identify mutational steps associated with significant phenotypic deviations. The central assumption behind this strategy is that any undetected mutation causing a phenotypic effect is embedded within the same evolutionary history that is represented by the cladogram. The power of this approach depends upon the confidence one has in the particular cladogram used to draw inferences. In this paper, we present a strategy for estimating the set of cladograms that are consistent with a particular sample of either restriction site or nucleotide sequence data and that includes the possibility of recombination. We first evaluate the limits of parsimony in constructing cladograms. Once these limits have been determined, we construct the set of parsimonious and nonparsimonious cladograms that is consistent with these limits. Our estimation procedure also identifies haplotypes that are candidates for being products of recombination. If recombination is extensive, our algorithm subdivides the DNA region into two or more subsections, each having little or no internal recombination. We apply this estimation procedure to three data sets to illustrate varying degrees of cladogram ambiguity and recombination.
3,071 citations
"TCS: a computer program to estimate..." refers methods in this paper
...The method of Templeton et al. (1992) (TCS) has been used extensively with restriction site and nucleotide sequence data to infer population level genealogies when divergences are low (Georgiadis et al ....
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TL;DR: It is shown that nested phylogeographical analyses have more power to detect geographical associations than traditional, nonhistorical analyses and, as a consequence, allow a broader range of gene‐flow parameters to be estimated in a precise fashion.
Abstract: Since the 1920s, population geneticists have had measures that describe how genetic variation is distributed spatially within a species’ geographical range. Modern genetic survey techniques frequently yield information on the evolutionary relationships among the alleles or haplotypes as well as information on allele frequencies and their spatial distributions. This evolutionary information is often expressed in the form of an estimated haplotype or allele tree. Traditional statistics of population structure, such as F statistics, do not make use of evolutionary genealogical information, so it is necessary to develop new statistical estimators and tests that explicitly incorporate information from the haplotype tree. One such technique is to use the haplotype tree to define a nested series of branches (clades), thereby allowing an evolutionary nested analysis of the spatial distribution of genetic variation. Such a nested analysis can be performed regarding the geographical sampling locations either as categorical or continuous variables (i.e. some measure of spatial distance). It is shown that such nested phylogeographical analyses have more power to detect geographical associations than traditional, nonhistorical analyses and, as a consequence, allow a broader range of gene-flow parameters to be estimated in a precise fashion. More importantly, such nested analyses can discriminate between phylogeographical associations due to recurrent but restricted gene flow vs. historical events operating at the population level (e.g. past fragmentation, colonization, or range expansion events). Restricted gene flow and historical events can be intertwined, and the cladistic analyses can reconstruct their temporal juxtapositions, thereby yielding great insight into both the evolutionary history and population structure of the species. Examples are given that illustrate these properties, concentrating on the detection of range expansion events.
1,200 citations
"TCS: a computer program to estimate..." refers background or methods in this paper
...1995; Templeton 1998) and explore the phylogeographic history of a diversity of organisms (e.g. Johnson & Jordon 2000; Turner et al ....
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...The approach has also been used extensively with a nested analysis procedure to partition population structure from population history (Templeton et al . 1995; Templeton 1998) and explore the phylogeographic history of a diversity of organisms (e....
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TL;DR: This paper shows how a nested cladistic analysis of geographical distances can be used to test the null hypothesis of no geographical association of haplotypes, test the hypothesis that significant associations are due to restricted gene flow, and identify patterns of significant association that is due to historical events.
Abstract: Nonrandom associations of alleles or haplotypes with geographical location can arise from restricted gene flow, historical events (fragmentation, range expansion, colonization), or any mixture of these factors. In this paper, we show how a nested cladistic analysis of geographical distances can be used to test the null hypothesis of no geographical association of haplotypes, test the hypothesis that significant associations are due to restricted gene flow, and identify patterns of significant association that are due to historical events. In this last case, criteria are given to discriminate among contiguous range expansion, long-distance colonization, and population fragmentation. The ability to make these discriminations depends critically upon an adequate geographical sampling design. These points are illustrated with a worked example: mitochondrial DNA haplotypes in the salamander Ambystoma tigrinum. For this example, prior information exists about restricted gene flow and likely historical events, and the nested cladistic analyses were completely concordant with this prior information. This concordance establishes the plausibility of this nested cladistic approach, but much future work will be necessary to demonstrate robustness and to explore the power and accuracy of this procedure.
1,164 citations
TL;DR: A novel network approach for portraying mtDNA relationships is proposed that reduces the complexity of the network by identifying parallelisms and is guided by a compatibility argument and an additional source of phylogenetic information: the frequencies of the mitochondrial haplotypes.
Abstract: Analysis of variation in the hypervariable region of mitochondrial DNA (mtDNA) has emerged as an important tool for studying human evolution and migration. However, attempts to reconstruct optimal intraspecific mtDNA phylogenies frequently fail because parallel mutation events partly obscure the true evolutionary pathways. This makes it inadvisable to present a single phylogenetic tree at the expense of neglecting equally acceptable ones. As an alternative, we propose a novel network approach for portraying mtDNA relationships. For small sample sizes (< approximately 50), an unmodified median network contains all most parsimonious trees, displays graphically the full information content of the sequence data, and can easily be generated by hand. For larger sample sizes, we reduce the complexity of the network by identifying parallelisms. This reduction procedure is guided by a compatibility argument and an additional source of phylogenetic information: the frequencies of the mitochondrial haplotypes. As a spin-off, our approach can also assist in identifying sequencing errors, which manifest themselves in implausible network substructures. We illustrate the advantages of our approach with several examples from existing data sets.
1,092 citations