Species-Level Paraphyly and Polyphyly: Frequency, Causes, and Consequences, with Insights from Animal Mitochondrial DNA

@article{Funk2003SpeciesLevelPA,
  title={Species-Level Paraphyly and Polyphyly: Frequency, Causes, and Consequences, with Insights from Animal Mitochondrial DNA},
  author={Daniel J. Funk and Kevin E Omland},
  journal={Annual Review of Ecology, Evolution, and Systematics},
  year={2003},
  volume={34},
  pages={397-423}
}
▪ Abstract Many uses of gene trees implicitly assume that nominal species are monophyletic in their alleles at the study locus. However, in well-sampled gene trees, certain alleles in one species may appear more closely related to alleles from different species than to other conspecific alleles. Such deviations from species-level monophyly have a variety of causes and may lead to erroneous evolutionary interpretations if undetected. The present paper describes the causes and consequences of these paraphyletic and polyphyletic patterns. It also provides a detailed literature survey of mitochondrial DNA studies on low-level animal phylogeny and phylogeography, results from which reveal the frequency of nonmonophyly and patterns of interpretation and sampling. [] Key Result This survey detected species-level paraphyly or polyphyly in 23% of 2319 assayed species, demonstrating this phenomenon to be statistically supported, taxonomically widespread, and far more common than generally recognized. Our findings call for increa...

Figures and Tables from this paper

The incidence of species-level paraphyly in animals: a re-assessment.
  • H. Ross
  • Biology
    Molecular phylogenetics and evolution
  • 2014
Widespread genealogical nonmonophyly in species of Pinus subgenus Strobus.
TLDR
It is felt that incomplete lineage sorting remains the best explanation for the polymorphisms shared among species, and taxa sharing similar life history traits with Pinus are likely to show species nonmonophyly using nuclear markers.
Sequence-based species delimitation for the DNA taxonomy of undescribed insects.
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
Geographic Life History Differences Predict Genomic Divergence Better than Mitochondrial Barcodes or Phenotype
TLDR
It is found that geographically associated life history factors better predict genomic divergence than phenotype and mitochondrial genealogies, and consequently taxon identifications based on mtDNA (e.g., DNA barcodes) may be misleading.
Discordance between genomic divergence and phenotypic variation in a rapidly evolving avian genus (Motacilla).
Divergent clades or cryptic species? Mito-nuclear discordance in a Daphnia species complex
TLDR
The occurrence of highly divergent but rare mtDNA lineages in the gene pool of widespread species would suggest that hybridization and introgression in the D. longispina species complex is frequent even across large phylogenetic distances, and that discoveries of such distinct clades must be interpreted with caution.
Ancient hybridization and mitochondrial capture between two species of chipmunks
TLDR
Overall, these data indicate that introgression has had a minimal impact on the nuclear genomes of T. amoenus and T. ruficaudus despite multiple independent hybridization events, and suggest that there may be other examples of hybridization among the 23 species of Tamias that occur in western North America.
The application of molecular data to the phylogenetic delimitation of species in bryophytes: A note of caution
TLDR
This work makes some suggestions about how to use molecular data in the circumscription of bryophyte species, and encourages case by case evaluation of all available data rather than applying a single criterion such as monophyly.
Species-Level Para- and Polyphyly in DNA Barcode Gene Trees: Strong Operational Bias in European Lepidoptera
TLDR
It is suggested that species-level non-monophyly in COI gene trees is less common than previously supposed, with many cases reflecting misidentifications, the subjectivity of species delimitation or other operational factors.
...
...

References

SHOWING 1-10 OF 143 REFERENCES
Paraphyly, polyphyly, and the nature of species boundaries in pocket gophers (Genus Thomomys)
TLDR
A set of problems with data on mitochondrial DNA sequences and both nuclear sequences and allozyme electromorphs for sets of populations of two currently recognized species of pocket gophers, Thomomys bottae and T. townsendii in the western United States is illustrated.
Gene Trees and Species Trees: Molecular Systematics as One-Character Taxonomy
TLDR
A character phylogeny, in this case a gene tree, can be tested best by a parsimony analysis in which other characters are included, and each is an equivalent phylogenetic hypothesis, as is each non-molecular character, leading to the suggestion that direct combination is appropriate.
Mitochondrial DNA differentiation during the speciation process in Peromyscus.
TLDR
The theoretical and empirical results for mtDNA in maniculatus and polionotus appear to conform closely to case III, and it is suggested that the distribution patterns of mtDNA sequence variation within and among extant species should be of considerable relevance to the particular demographies of speciation.
mtDNA diversity in rhesus monkeys reveals overestimates of divergence time and paraphyly with neighboring species.
TLDR
It is concluded that intraspecific mtDNA diversity is substantial in at least some primate species, and the reliability of hominoid mtDNA phylogenies, based as they are on one or a few representatives of each species, in an already depauperate superfamily of primates is questioned.
When one is not enough: introgression of mitochondrial DNA in Drosophila.
  • J. Ballard
  • Biology
    Molecular biology and evolution
  • 2000
The specific purpose of this study is to investigate alternate processes that may have resulted in the formation of the two distinct mitochondrial haplotypes (maI and maII) of Drosophila mauritiana.
MITOCHONDRIAL GENE TREES AND THE EVOLUTIONARY RELATIONSHIP OF MALLARD AND BLACK DUCKS
TLDR
Overall, the mtDNA data indicate an extremely close evolutionary relationship between Mallards and Black Ducks, and in conjunction with the geographic distributions suggest that the Black Duck is a recent evolutionary derivative of a more broadly distributed Mallard‐Black ancestor.
Molecular systematics of cytochrome oxidase I and 16S from Neochlamisus leaf beetles and the importance of sampling.
  • D. J. Funk
  • Biology
    Molecular biology and evolution
  • 1999
TLDR
By subsampling haplotypes corresponding to particular species, populations, and ecological variants of gibbosus group taxa, it is demonstrated that recovered topologies and genetic distances vary egregiously according to sampling regime.
GENE TREES AND ORGANISMAL HISTORIES: A PHYLOGENETIC APPROACH TO POPULATION BIOLOGY
  • J. Avise
  • Biology
    Evolution; international journal of organic evolution
  • 1989
TLDR
Preliminary extensions of the “gene tree” methodology to haplotypes of nuclear genes demonstrate that the phylogenetic perspective can also help to illuminate molecular‐genetic processes (such as recombination or gene conversion), as well as contribute to knowledge of the origin, age, and molecular basis of particular adaptations.
Trees within trees: genes and species, molecules and morphology.
TLDR
Linkage relationships limit character independence and thus have important implications for handling multiple data sets in phylogenetic analysis, particularly at the species level, where incongruence among different historically associated loci is expected.
Comparison of Y chromosome and mtDNA phylogenies leads to unique inferences of macaque evolutionary history.
TLDR
The results of one of the first analyses to use male-specific nuclear markers in elucidating primate phylogenetic relationships at the intrageneric level raise the question of whether a phylogenetic tree should be a topology of species origins or a depiction of more current species relationships, including subsequent episodes of introgression.
...
...