author={Scott V. Edwards and Peter Beerli},
Molecular methods as applied to the biogeography of single species (phylogeography) or multiple codistributed species (comparative phylogeography) have been productively and extensively used to elucidate common historical features in the diversification of the Earth's biota. However, only recently have methods for estimating population divergence times or their confidence limits while taking into account the critical effects of genetic polymorphism in ancestral species become available, and… 


Using genealogical patterns in mitochondrial DNA and in introns of four nuclear loci to test for historical bottlenecks during the speciation and divergence of two temperate Lagenorhynchus dolphin species isolated by tropical Pacific waters, a parsimonious model for the Pleistocene origin of these distributions would not involve rare breaches of a constant dispersal barrier by small colonization propagules.

Divergence genetics analysis reveals historical population genetic processes leading to contrasting phylogeographic patterns in co‐distributed species

Traditional characterizations of population structure and coalescent‐based inferences about demographic processes are used to reconstruct the population histories of two co‐distributed marine species, the frilled dog whelk, Nucella lamellosa, and the bat star, Patiria miniata, finding gene flow was greater in bat stars than snails but spatially homogeneous within species.

Influence of gene flow on divergence dating – implications for the speciation history of Takydromus grass lizards

It is demonstrated that gene flow during the speciation process cannot be overlooked and may have a great impact on divergence dating, and a more biologically realistic framework for delineating the divergence history of Takydromus is provided.

Genomic variation in a widespread Neotropical bird (Xenops minutus) reveals divergence, population expansion, and gene flow.

Examining the Role of Effective Population Size on Mitochondrial and Multilocus Divergence Time Discordance in a Songbird

The findings of this study indicate that in phylogeographic studies the relative tempo of evolution between mtDNA and nuclear DNA can become highly discordant in small populations.

Resolving Species Phylogenies of Recent Evolutionary Radiations1

Differences in the ability to recover species relationships across multiple simulated species trees highlight the potential effects of taxon sampling on phylogenetic inference at, or near, the species boundary and under high rates of speciation.

Multispecies Coalescent Analysis of the Early Diversification of Neotropical Primates: Phylogenetic Inference under Strong Gene Trees/Species Tree Conflict

It is shown, by multispecies coalescent analyses of selected genome segments, that the early diversification of extant NP was marked by a 2-fold increase of their effective population size and that Atelids and Cebids are more closely related respective to Pitheciids.

A species assemblage approach to comparative phylogeography of birds in southern Australia

A novel approach to investigating the divergence history of biomes and their component species using single-locus data prior to investing in multilocus data, using the power of multitaxa coalescent analyses as an efficient means of generating a foundation for further, targeted research.


  • L. KnowlesB. Carstens
  • Biology, Environmental Science
    Evolution; international journal of organic evolution
  • 2007
It is indicated that sampling of multiple individuals per population is critical to obtaining an accurate estimate of the history of divergence so that the signal of common ancestry can be separated from the confounding influence of gene flow—even though estimates suggest that gene flow is not a predominant factor structuring patterns of genetic variation across these sky island populations.



Comparative mtDNA phylogeography of neotropical freshwater fishes: testing shared history to infer the evolutionary landscape of lower Central America

The fisheye view of LCA suggests a complex biogeographic history of overlaid cycles of colonization, diversification, sorting and extinction of lineages, a pattern the authors attribute to the continuing development of the landscape due to orogeny and the consequent increase in the insularization of drainage basins.

Pleistocene effects on North American songbird evolution

  • J. KlickaR. M. Zink
  • Biology
    Proceedings of the Royal Society of London. Series B: Biological Sciences
  • 1999
The study used the average interphylogroup mtDNA distance, calibrated at 2% per million years, to conclude that speciation required on average one million years to complete, which means speciation events begun in the Late Pliocene would have been completed in the mid– to late Pleistocene.

Comparative phylogeography: concepts and applications

This issue projects that comparative phylogeographic analysis will permit detailed studies of landscape evolution, including the dispersal of taxa through a region, speciation, adaptive radiation, and extinction; in other words, investigation of the fundamental links between population processes and regional patterns of diversity and biogeography.

Molecular phylogeography and the evolution and conservation of Amazonian mammals

The phylogeographic structure of 15 genera of Amazonian marsupials and rodents is summarized based on comparative sequence of the mitochondrial cytochrome b gene, and patterns of concordant geographical shifts with underlying tectonic history and to current positions of major rivers are related.

Divergence time and population size in the lineage leading to modern humans.

The ML analysis of two species shows that humans Diverged from chimpanzees 4.6 my ago and that the human and chimpanzee clade diverged from the gorilla 7.2 my ago, and the effective population size of humans more than 4.

Pleistocene phylogeographic effects on avian populations and the speciation process

  • J. AviseD. Walker
  • Biology
    Proceedings of the Royal Society of London. Series B: Biological Sciences
  • 1998
When avian speciation is viewed properly as an extended temporal process rather than as a point event, Pleistocene conditions appear to have played an active role both in initiating major phylogeographic separations within species, and in completing speciations that had been inaugurated earlier.

Developing model systems for molecular biogeography: Vicariance and interchange in marine invertebrates

This chapter focuses on studies of littoral marine invertebrates in three well-studied marine model systems, and presents molecular divergence, population genetic, and in some cases, paleontological evidence that sister taxa in neighboring areas likely diverged at different times.

Molecular population structure and the biogeographic history of a regional fauna : a case history with lessons for conservation biology

  • J. Avise
  • Biology, Environmental Science
  • 1992
These concordant phylogeographic patterns among independently evolving species provide evidence of similar vicariant histories of population separation, and can be related tentatively to episodic changes in environmental conditions during the Pleistocene.

New dates and new rates for divergence across the Isthmus of Panama

  • N. KnowltonL. Weigt
  • Biology
    Proceedings of the Royal Society of London. Series B: Biological Sciences
  • 1998
Patterns of divergence exhibited by allozymes and the mitochondrial COI gene are highly concordant for 15 pairs of snapping shrimp in the genus Alpheus, indicating that they provide a reasonable basis for estimating time since cessation of gene flow.

Evolution of the primate lineage leading to modern humans: phylogenetic and demographic inferences from DNA sequences.

  • N. TakahataY. Satta
  • Biology
    Proceedings of the National Academy of Sciences of the United States of America
  • 1997
It is argued that the human ancestral lineage branched off from the NWM and OWM earlier than once thought and that significant demographic changes might have occurred at different evolutionary stages, particularly at the hominid stage.