Pleistocene speciation in the genus Populus (salicaceae).

The macroevolutionary consequences of recent climate change remain controversial, and there is little paleobotanical or morphological evidence that Pleistocene (1.8-0.12 Ma) glacial cycles acted as drivers of speciation, especially among lineages with long generation times, such as trees. We combined genetic and ecogeographic data from 2 closely related North American tree species, Populus balsamifera and P. trichocarpa (Salicacaeae), to determine if their divergence coincided with and was possibly caused by Pleistocene climatic events. We analyzed 32 nuclear loci from individuals of P. balsamifera and P. trichocarpa to produce coalescent-based estimates of the divergence time between the 2 species. We coupled the coalescent analyses with paleodistribution models to assess the influence of climate change on species' range. Furthermore, measures of niche overlap were used to investigate patterns of ecological differentiation between species. We estimated the divergence date of P. balsamifera and P. trichocarpa at approximately 75 Ka, which corresponds closely with the onset of Marine Isotope Stage 4 (∼76 Ka) and a rapid increase in global ice volume. Significance tests of niche overlap, in conjunction with genetic estimates of migration, suggested that speciation occurred in allopatry, possibly resulting from the environmental effects of Pleistocene glacial cycles. Our results indicate that the divergence of keystone tree species, which have shaped community diversity in northern North American ecosystems, was recent and may have been a consequence of Pleistocene-era glaciation and climate change.

Nei's to Bayes': comparing computational methods and genetic markers to estimate patterns of genetic variation in Tolpis (Asteraceae).

Accurate determination of patterns of genetic variation provides a powerful inferential tool for studies of evolution and conservation. For more than 30 years, enzyme electrophoresis was the preferred method for elucidating these patterns. As a result, evolutionary geneticists have acquired considerable understanding of the relationship between patterns of allozyme variation and aspects of evolutionary process. Myriad molecular markers and statistical analyses have since emerged, enabling improved estimates of patterns of genetic diversity. With these advances, there is a need to evaluate results obtained with different markers and analytical methods. We present a comparative study of gene statistic estimates (F(ST), G(ST), F(IS), H(S), and H(T)) calculated from an intersimple sequence repeat (ISSR) and an allozyme data set derived from the same populations using both standard and Bayesian statistical approaches. Significant differences were found between estimates, owing to the effects of marker and analysis type. Most notably, F(ST) estimates for codominant data differ between Bayesian and standard approaches. Levels of statistical significance are greatly affected by methodology and, in some cases, are not associated with similar levels of biological significance. Our results suggest that caution should be used in equating or comparing results obtained using different markers and/or methods of analysis.

Inferring phylogeny at low taxonomic levels: utility of rapidly evolving cpDNA and nuclear ITS loci.

Plant molecular systematic studies of closely related taxa have relied heavily on sequence data from nuclear ITS and cpDNA. Positive attributes of using ITS sequence data include the rapid rate of evolution compared to most plastid loci and availability of universal primers for amplification and sequencing. On the other hand, ITS sequence data may not adequately track organismal phylogeny if concerted evolution and high rDNA array copy number do not permit identification of orthologous copies. Shaw et al. (American Journal of Botany 92: 142-166) recently identified nine plastid regions that appear to provide more potentially informative characters than many other plastid loci. In the present study, sequences of these loci and ITS were obtained for six taxonomic groups in which phylogenetic relationships have been difficult to establish using other data. The relative utility of these regions was compared by assessing the number of parsimony informative characters, character congruence, resolution of inferred trees, clade support, and accuracy. No single locus emerged as the best in all lineages for any of these measures of utility. Results further indicated that in preliminary studies, sampling strategy should include at least four exemplar taxa. The importance of sampling data from independent distributions is also discussed.