Population genetic structure and hybridization patterns in the Mediterranean endemics Phlomis lychnitis and P. crinita (Lamiaceae)

BACKGROUND AND AIMS: The historical influence of gene flow and genetic drift after the last glacial phase of the Quaternary Period is reflected in current levels of genetic diversity and population structure of plant species. Moreover, hybridization after secondary contact might also affect population genetic diversity and structure. An assessment was made of the genetic variation and hybrid zone structure in Iberian populations of the Mediterranean Phlomis lychnitis and P. crinita, for which phylogenetic relationships are controversial, and hybridization and introgression are common. METHODS: Allozyme variation at 13 loci was analysed in 1723 individual plants sampled from 35 natural locations of P. lychnitis, P. crinita subsp. malacitana and P. crinita subsp. crinita in southern and eastern Spain. Standard genetic diversity parameters were calculated and patterns of genetic structure in each taxon were tested to fit the equilibrium between gene flow and genetic drift. Individual multilocus genotypes were subjected to Bayesian clustering analysis to estimate hybridization and introgression rates for both geographic regions. KEY RESULTS: Contrasting patterns in the distribution of genetic variation among the three taxa were found. Phlomis lychnitis showed no significant inbreeding, low genetic differentiation among populations and no evidence of isolation by distance. Phlomis crinita subsp. malacitana and P. crinita subsp. crinita showed high levels of genetic structure consistent with a pattern of gene flow-drift equilibrium. Higher instances of hybridization and introgression were detected in locations from southern Spain compared with locations from eastern Spain, matching unimodal and bimodal hybrid zones, respectively. CONCLUSIONS: High instances of historical gene flow, range expansion and altitudinal movement during the Quaternary Period, and lineage sorting can explain the diversity of patterns observed. The results suggest that P. lychnitis is the most differentiated lineage in the group; however, the relationship between the three taxa remains unclear.     

Examining genetic structure in a bogus yucca moth: a sequential approach to phylogeography

Understanding the phylogeography of a species requires not only elucidating patterns of genetic structure among populations, but also identifying the possible evolutionary events creating that structure. The use of a single phylogeographic test or analysis, however, usually provides a picture of genetic structure without revealing the possible underlying evolutionary causes. We used current analytical techniques in a sequential approach to examine genetic structure and its underlying causes in the bogus yucca moth Prodoxus decipiens (Lepidoptera: Prodoxidae). Both historical biogeography and recent human transplantations of the moth's host plants provided a priori expectations of the pattern of genetic structure and its underlying causes. We evaluated these expectations by using a progression of phylogenetic, demographic, and population genetic analyses of mtDNA sequence data from 476 individuals distributed across 25 populations that encompassed the range of P. decipiens. The combination of these analyses revealed that much of the genetic structure has evolved more recently than suggested by historical biogeography, has been influenced by changes in demography, and can be best explained by long distance dispersal and isolation by distance. We suggest that performing a suite of analyses that focus on different temporal scales may be an effective approach to investigating the patterns and causes of genetic structure within species.     

Population genetic structure of the catadromous Australian bass from throughout its range

One hatchery-derived impoundment and nine wild riverine populations of the catadromous percoid Australian bass Macquaria novemaculeata were examined at six polymorphic allozyme loci to reveal population genetic structure. Subtle genetic differences among many populations indicated that fish did not interact as a panmictic unit, but rather conformed to an isolation by distance pattern of population structure. The hatchery-derived Glenbawn Dam sample differed from the riverine populations in both average heterozygosity and number of polymorphic loci, demonstrating the need for caution in supplementation programs to rehabilitate wild riverine populations.     

Landscape genetic structure of Scirpus mariqueter reveals a putatively adaptive differentiation under strong gene flow in estuaries

Estuarine organisms grow in highly heterogeneous habitats, and their genetic differentiation is driven by selective and neutral processes as well as population colonization history. However, the relative importance of the processes that underlie genetic structure is still puzzling. Scirpus mariqueter is a perennial grass almost limited in the Changjiang River estuary and its adjacent Qiantang River estuary. Here, using amplified fragment length polymorphism (AFLP), a moderate‐high level of genetic differentiation among populations (range F_ST: 0.0310–0.3325) was showed despite large ongoing dispersal. FLOCK assigned all individuals to 13 clusters and revealed a complex genetic structure. Some genetic clusters were limited in peripheries compared with very mixing constitution in center populations, suggesting local adaptation was more likely to occur in peripheral populations. 21 candidate outliers under positive selection were detected, and further, the differentiation patterns correlated with geographic distance, salinity difference, and colonization history were analyzed with or without the outliers. Combined results of AMOVA and IBD based on different dataset, it was found that the effects of geographic distance and population colonization history on isolation seemed to be promoted by divergent selection. However, none‐liner IBE pattern indicates the effects of salinity were overwhelmed by spatial distance or other ecological processes in certain areas and also suggests that salinity was not the only selective factor driving population differentiation. These results together indicate that geographic distance, salinity difference, and colonization history co‐contributed in shaping the genetic structure of S. mariqueter and that their relative importance was correlated with spatial scale and environment gradient.     

Population genetic structure and phylogeography of the oak gall wasp Andricus chodjaii (Hymenoptera: Cynipidae) in Turkey as inferred from mitochondrial and nuclear DNA sequences

Sequence data of mitochondrial cytochrome b gene and nuclear ITS2 region were used to assess genetic diversity, intraspecific phylogeography and population genetic structure of the oak gall wasp Andricus chodjaii from Turkey. We examined 293 individuals from 21 localities which generated 57 cyt b haplotypes and 8 ITS2 alleles. The average genetic diversity was 0.575 for cyt b and 0.202 ITS2, and the average nucleotide diversity 0.015 for cyt b gene and 0.001 for the ITS2 region. Phylogenetic analyses of cyt b haplotypes produced mostly similar topologies with geographically significant groupings. The ITS2 data provided less resolution without robust and apparent geographic structure. Population demographic analysis indicated that some eastern populations expanded, however, some others underwent either expansion or decline resulting in genetically structured populations. Molecular clock applied to the mtDNA data indicated that ingroup haplotypes diversified from the outgroup haplotypes around Early Pliocene. Further diversification events throughout Pleistocene resulted in major clade formations. It appears that geographic formations and glacial and interglacial cycles of Pleistocene were crucial for shaping the phylogeographic structure of A. chodjaii in Turkey.     

Isolation by distance and sharp discontinuities in gene frequencies: implications for the phylogeography of an alpine insect species, Carabus solieri

Analysis of genetic isolation by distance (IBD) is of prime importance for the study of processes responsible for spatial population genetic structure and is thus frequently used in case studies. However, the identification of a significant IBD pattern does not necessarily imply the absence of sharp discontinuities in gene frequencies. Therefore, identifying barriers to gene flow and/or secondary contact between differentiated entities remains a major challenge in population biology. Geographical genetic structure of 41 populations (1080 individuals) of an alpine insect species, Carabus solieri, was studied using 10 microsatellite loci. All populations were significantly differentiated and spatially structured according to IBD over the entire range. However, clustering analyses clearly identified three main clusters of populations, which correspond to geographical entities. Whereas IBD also occurs within each cluster, population structure was different according to which group of populations was considered. The southernmost cluster corresponds to the most fragmented part of the range. Consistently, it was characterized by relatively high levels of differentiation associated with low genetic diversity, and the slope of the regression of genetic differentiation against geographical distances was threefold those of the two other clusters. Comparisons of within-cluster and between-cluster IBD patterns revealed barriers to gene flow. A comparison of the two approaches, IBD and clustering analyses, provided us with valuable information with which to infer the phylogeography of the species, and in particular to propose postglacial colonization routes from two potential refugia located in Italy and in southeastern France. Our study highlights strongly the possible confounding contribution of barriers to gene flow to IBD pattern and emphasizes the utility of the model-based clustering analysis to identify such barriers.     

Fine-scale spatial genetic structure and gene dispersal in Silene latifolia

Plants are sessile organisms, often characterized by limited dispersal. Seeds and pollen are the critical stages for gene flow. Here we investigate spatial genetic structure, gene dispersal and the relative contribution of pollen vs seed in the movement of genes in a stable metapopulation of the white campion Silene latifolia within its native range. This short-lived perennial plant is dioecious, has gravity-dispersed seeds and moth-mediated pollination. Direct measures of pollen dispersal suggested that large populations receive more pollen than small isolated populations and that most gene flow occurs within tens of meters. However, these studies were performed in the newly colonized range (North America) where the specialist pollinator is absent. In the native range (Europe), gene dispersal could fall on a different spatial scale. We genotyped 258 individuals from large and small (15) subpopulations along a 60 km, elongated metapopulation in Europe using six highly variable microsatellite markers, two X-linked and four autosomal. We found substantial genetic differentiation among subpopulations (global F_ST=0.11) and a general pattern of isolation by distance over the whole sampled area. Spatial autocorrelation revealed high relatedness among neighboring individuals over hundreds of meters. Estimates of gene dispersal revealed gene flow at the scale of tens of meters (5–30 m), similar to the newly colonized range. Contrary to expectations, estimates of dispersal based on X and autosomal markers showed very similar ranges, suggesting similar levels of pollen and seed dispersal. This may be explained by stochastic events of extensive seed dispersal in this area and limited pollen dispersal.     

Population structure of odd-broodline Asian pink salmon and its contrast to the even-broodline structure

Most of the variation (99%) of Asian odd-broodline pink salmon Oncorhynchus gorbuscha , based on data at 32 variable (46 total) allozyme loci from 35 populations, occurred within populations. The remaining interpopulation variation was attributable to: (1) differences between northern (the northern Sea of Okhotsk, eastern Kamchatka Peninsula and western Kamchatka Peninsula) and southern (Hokkaido Island, Kuril Islands and Sakhalin Island) populations; (2) differences between the southern areas; (3) low variation among populations within some areas. The pattern contrasted strongly with that observed for Asian even-broodline populations, which had a strong structure, possibly related to geographic and oceanographic influences. Isolation-by-distance analyses of each of the two broodlines showed a stronger relationship (x 4·8) among even- than odd-broodline populations. Allele frequency differences between even- and odd-broodlines reflected the reproductive isolation of the broodlines. However, there were no fixed frequency differences which, considered with the differing population structures, suggests that migration-drift equilibrium has not yet obtained in one or both broodlines. The structural differences also suggest it is likely that the even- and odd-broodlines are of different ages and that one is derived from the other. Allozyme data do not provide a genealogical basis for identifying the ancestral lineage.     

Population structure and genetic variability of pearl oyster Pinctada mazatlanica along Pacific coasts from Mexico to Panama

Populations of the Calafia pearl oyster Pinctada mazatlanica ofthe American Pacific coasts have been considered endangeredbecause of overfishing and/or alteration to coastal areas. Weassessed genetic variability and the pattern of populationstructure among 9 samples collected from Mexico to Panama, usingmtDNA RFLP analysis of two genes: 12S rRNA and subunit one ofCytochrome oxydase (COI). Haplotype diversity varied from 0.000to 0.856. The Panama population appeared to be monomorphic, whilethe other samples exhibited a level of haplotypic variabilitysimilar to those reported in the literature for the same kind ofanalysis on other bivalves species. A test for the impact ofdemographic history on genetic diversity was applied on thesequence data, and the results were congruent with a recentdecline of population sizes. Genetic differentiation was shown tofollow a scheme of isolation by distance, with low levels ofdifferentiation at the scales of ten to one hundred kilometres,whereas stronger and significant genetic structure was detectedat a larger scale. Three significantly distinct groups could thenbe defined, which correspond to Northern Mexico, Southern Mexico,and Panama.     

Phylogeny and phylogeography of Arenaria section Pseudomoehringia

Phylogeographic and evolutionary studies are necessary to establish solid taxonomic treatments and to implement effective conservation programs. Unfortunately, a well‐argued and well‐founded taxonomic framework is still lacking for some Mediterranean taxa. This is the case of Arenaria section Pseudomoehringia, a group that currently comprises three species endemic to the Iberian Peninsula (A. funiculata, A. suffruticosa, and A. tejedensis) and A. glochidisperma, which is restricted to the Rif mountains, North Africa. However, the taxonomic boundaries and phylogenetic relationships among these species are still uncertain. To explore the evolutionary history and phylogeographic patterns within this section, analyses based on nuclear (amplified fragment length polymorphism and internal transcribed spacer) and plastid DNA markers (psbA‐3’ trnK‐matK and rps16) were performed. Our study has confirmed the monophyly of the section, in which two species are clearly identified (A. funiculata and A. glochidisperma) and an additional species complex (“A. suffruticosa + A. tejedensis complex”) is also supported as a monophyletic clade. The phylogeographic results point toward a dispersal event of a common ancestor of the group from the Iberian Peninsula, giving rise to A. glochidisperma in North Africa. Moreover, A. funiculata and A. glochidisperma are identified as closely related species edaphically differentiated across the Strait of Gibraltar. Our study indicates low levels of a recent gene flow among populations of the “A. suffruticosa + A. tejedensis complex,” which are genetically highly structured and suggest an isolation by distance pattern, probably due to a combination of ecological and geographic barriers. Furthermore, the taxonomic and conservation status of taxa included in Arenaria section Pseudomoehringia has been reviewed.     

Different processes shape the patterns of divergence in the nuclear and chloroplast genomes of a relict tree species in East Asia

Isolation by spatial distance (IBD), environment (IBE), and historical climatic instability (IBI) are three common processes assessed in phylogeographic and/or landscape genetic studies. However, the relative contributions of these three processes with respect to spatial genetic patterns have seldom been compared. Moreover, whether the relative contribution differs in different regions or when assessed using different genetic markers has rarely been reported. Lindera obtusiloba has been found to have two sister genetic clades of chloroplast (cpDNA) and nuclear microsatellite (nSSR), both of which show discontinuous distribution in northern and southern East Asia. In this study, we used the Mantel test and multiple matrix regression with randomization (MMRR) to determine the relative contributions of IBD, IBE, and IBI with respect to L. obtusiloba populations. Independent Mantel tests and MMRR calculations were conducted for two genetic data sets (cpDNA and nSSR) and for different regions (the overall species range, and northern and southern subregions of the range). We found a significant IBI pattern in nSSR divergence for all assessed regions, whereas no clear IBI pattern was detected with respect to cpDNA. In contrast, significant (or marginal) divergent IBD patterns were detected for cpDNA in all regions, whereas although a significant IBE was apparent with respect to the overall range, the effect was not detected in the two subregions. The differences identified in nSSR and cpDNA population divergence may be related to differences in the heredity and ploidy of the markers. Compared with the southern region, the northern region showed less significant correlation patterns, which may be related to the shorter population history and restricted population range. The findings of this study serve to illustrate that comparing between markers or regions can contribute to gaining a better understanding the population histories of different genomes or within different regions of a species' range.     

Microsatellite analysis of the phylogeography, Pleistocene history and secondary contact hypotheses for the killifish, Fundulus heteroclitus

The mummichog, Fundulus heteroclitus, exhibits extensive latitudinal clinal variation in a number of physiological and biochemical traits, coupled with phylogeographical patterns at mitochondrial and nuclear DNA loci that suggest a complicated history of spatially variable selection and secondary intergradation. This species continues to serve as a model for understanding local and regional adaptation to variable environments. Resolving the influences of historical processes on the distribution of genetic variation within and among extant populations of F. heteroclitus is crucial to a better understanding of how populations evolve in the context of contemporary environments. In this study, we analysed geographical patterns of genetic variation at eight microsatellite loci among 15 populations of F. heteroclitus distributed throughout the North American range of the species from Nova Scotia to Georgia. Genetic variation in Northern populations was lower than in Southern populations and was strongly correlated with latitude throughout the species range. The most common Northern alleles at all eight loci exhibited concordant latitudinal clinal patterns, and the existence of an abrupt transition zone in allele frequencies between Northern and Southern populations was similar to that observed for mitochondrial DNA and allozyme loci. A significant pattern of isolation by distance was observed both within and between northern and southern regions. This pattern was unexpected, particularly for northern populations, given the recent colonization history of post-Pleistocene habitats, and was inconsistent with either a recent northward population expansion or a geographically restricted northern Pleistocene refugium. The data provided no evidence for recent population bottlenecks, and estimates of historical effective population sizes suggest that post-Pleistocene populations have been large throughout the species distribution. These results suggest that F. heteroclitus was broadly distributed throughout most of its current range during the last glacial event and that the abrupt transition in allele frequencies that separate Northern and Southern populations may reflect regional disequilibrium conditions associated with the post-Pleistocene colonization history of habitats in that region.     

Correlates of genetic differentiation and isolation by distance in 17 congeneric Silene species

The contemporary pattern of intraspecific genetic variation can indicate the relative role of gene flow and local differentiation in shaping the evolutionary history and future trajectory of a species. To assess the recent influence of contrasting life history and demographic characteristics on genetic structure within a group of closely related species, patterns of genetic differentiation (F(ST) and related statistics) and isolation by distance (IBD) were compared among 17 congeneric herbaceous plant species. Data came from 35 published studies of 16 species, and a previously unpublished analysis of chloroplast genetic variation in the rare endemic Silene rotundifolia. Among-population genetic variance was most strongly influenced by the type of genetic marker used; cytoplasmic markers showed larger values than allozyme and anonymous nuclear markers. Other independently significant factors were geographical range size and, for allozyme studies, reproductive system; in particular, endemism and hermaphroditism were associated with higher among-population genetic variance, whereas large native geographical range and dioecy were associated with lower among-population variance. Over equivalent spatial scales, dioecious populations also showed weaker IBD than hermaphrodites, perhaps because increased population transience and/or variance in the spatial pattern of gene flow are more closely associated with dioecy in this genus. Invasive populations had both highly variable among-population genetic variance, and no evidence for IBD, consistent with nonequilibrium conditions. Other analysed factors including predominant pollinator had no discernable influence on genetic structure or patterns of IBD. In general, this comparative approach appears to be valuable for synthesizing the complementary information provided by F-statistics and IBD, and for indicating the relative importance of particular biological factors in shaping genetic variation within different species of a closely related plant group.     

Genetic differences among three colour morphotypes of the black rockfish,Sebastes inermis,inferred from mtDNA and AFLP analyses

The genetic differences among three colour morphotypes of the black rockish, Sebastes inermis, were determined from mitochondrial DNA (mtDNA) and amplified fragment length polymorphisms (AFLP) analyses. In the AFLP analysis, each morphotype could be distinguished by the presence or absence matrix of five AFLP loci. These diagnostic loci indicated that the three morphotypes represented independent gene pools, indicating reproductive isolation. Furthermore, 14 significant frequency differences in AFLP fragments were observed between morphotypes A and B, 12 between morphotypes A and C and six between morphotypes B and C. These significant differences also supported the likelihood of reproductive isolation among the morphotypes. In the mtDNA analysis, variations in partial sequences of the control region failed to distinguish clearly between the three morphotypes, but restrictions of gene flow and genetic differentiation among the morphotypes were supported by significant FST estimates. The absence of diagnostic mtDNA differences in this study may have been due to introgressive hybridization among the morphotypes and/or incomplete lineage sorting, due to the recency of speciation.     

Population genetics and demographic inferences in a recovering shorebird,the African Black Oystercatcher Haematopus moquini

The extensive literature on the African Black Oystercatcher is a testament to what is now a conservation success story. Here we provide the first genetic insight into the population dynamics of this recovering shorebird and an assessment of genetic variation within the species using microsatellite markers. Although behavioural studies suggest strong natal philopatry, we found a single genetic cluster across all of the locations sampled and a significant signal of isolation by distance suggesting some geographical structuring. The microsatellite markers used in this study are useful at a population level, and the limited genetic variation detected is likely to be due to a low historical population size.     

The influence of landscape configuration and environment on population genetic structure in a sedentary passerine: insights from loci located in different genomic regions

The study of the factors structuring genetic variation can help to infer the neutral and adaptive processes shaping the demographic and evolutionary trajectories of natural populations. Here, we analyse the role of isolation by distance (IBD), isolation by resistance (IBR, defined by landscape composition) and isolation by environment (IBE, estimated as habitat and elevation dissimilarity) in structuring genetic variation in 25 blue tit (Cyanistes caeruleus) populations. We typed 1385 individuals at 26 microsatellite loci classified into two groups by considering whether they are located into genomic regions that are actively (TL; 12 loci) or not (NTL; 14 loci) transcribed to RNA. Population genetic differentiation was mostly detected using the panel of NTL. Landscape genetic analyses showed a pattern of IBD for all loci and the panel of NTL, but genetic differentiation estimated at TL was only explained by IBR models considering high resistance for natural vegetation and low resistance for agricultural lands. Finally, the absence for IBE suggests a lack of divergent selection pressures associated with differences in habitat and elevation. Overall, our study shows that markers located in different genomic regions can yield contrasting inferences on landscape‐level patterns of realized gene flow in natural populations.     

Population structure attributable to reproductive time: isolation by time and adaptation by time

Many populations are composed of a mixture of individuals that reproduce at different times, and these times are often heritable. Under these conditions, gene flow should be limited between early and late reproducers, even within populations having a unimodal temporal distribution of reproductive activity. This temporal restriction on gene flow might be called "isolation by time" (IBT) to acknowledge its analogy with isolation by distance (IBD). IBD and IBT are not exactly equivalent, however, owing to differences between dispersal in space and dispersal in time. We review empirical studies of natural populations that provide evidence for IBT based on heritabilities of reproductive time and on molecular genetic differences associated with reproductive time. When IBT is present, variation in selection through the reproductive season may lead to adaptive temporal variation in phenotypic traits [adaptation by time (ABT)]. We introduce a novel theoretical model that shows how ABT increases as (i) selection on the trait increases; (ii) environmental influences on reproductive time decrease; (iii) the heritability of reproductive time increases; and (iv) the temporal distribution of reproductive activity becomes increasingly uniform. We then review empirical studies of natural populations that provide evidence for ABT by documenting adaptive temporal clines in phenotypic traits. The best evidence for IBT and ABT currently comes from salmonid fishes and flowering plants, but we expect that future work will show these processes are more widespread.     

Genetic population structure of the Dakota skipper (Lepidoptera: Hesperia dacotae): A North American native prairie obligate

A range-wide survey of Dakotaskipper (Hesperia dacotae) populationsassessed levels of genetic variability andgeographic scale of population structure inthis species of conservation concern. Thisspecies exists on isolated patches of nativetall- and mixed-grass prairie within a highlymodified landscape dominated by agriculture. It has been extirpated from the southernportion of its range and has sufferedrange-wide declines. Nine populations weresampled from western Minnesota, eastern SouthDakota, and southern Manitoba. Starch gelelectrophoresis was used to resolve 21 isozymeloci in 278 Dakota skippers. Dakota skipperpopulations were approximately as variable asother lepidopterans found in isolated habitats. Genetic distances indicated that Manitobapopulations were somewhat distinct from ones inMinnesota and South Dakota. Isolation-by-distance was detected range-wideand among the seven southern-most populations. Genetically effective immigration rates weresmall at both range-wide and regional scalesand effective populations sizes were lowsuggesting that Dakota skipper populations aregenetically isolated from one another, althoughthey were likely more connected in the recentpast. Genotype assignment tests revealed twoclusters of populations in Minnesota and SouthDakota that were not apparent from theisolation-by-distance results. Significantheterozygote deficiencies relative toHardy-Weinberg expectations and high inbreedingcoefficients suggest structure within samplelocations. Management recommendations includethe maximization of effective population sizein each Dakota skipper population to offset theeffects of drift and habitat corridors in somecases. Habitat management should consider thewithin-site population structure and possibletemporal population structure detected in thisstudy.     

Multiple nuclear gene sequences identify phylogenetic species boundaries in the rapidly radiating clade of Mexican ambystomatid salamanders

Delimiting the boundaries of species involved in radiations is critical to understanding the tempo and mode of lineage formation. Single locus gene trees may or may not reflect the underlying pattern of population divergence and lineage formation, yet they constitute the vast majority of the empirical data in species radiations. In this study we make use of an expressed sequence tag (EST) database to perform nuclear (nDNA) and mitochondrial (mtDNA) genealogical tests of species boundaries in Ambystoma ordinarium, a member of an adaptive radiation of metamorphic and paedomorphic salamanders (the Ambystoma tigrinum complex) that have diversified across terrestrial and aquatic environments. Gene tree comparisons demonstrate extensive nonmonophyly in the mtDNA genealogy of A. ordinarium, while seven of eight independent nuclear loci resolve the species as monophyletic or nearly so, and diagnose it as a well-resolved genealogical species. A differential introgression hypothesis is supported by the observation that western A. ordinarium localities contain mtDNA haplotypes that are identical or minimally diverged from haplotypes sampled from a nearby paedomorphic species, Ambystoma dumerilii, while most nDNA trees place these species in distant phylogenetic positions. These results provide a strong example of how historical introgression can lead to radical differences between gene trees and species histories, even among currently allopatric species with divergent life history adaptations and morphologies. They also demonstrate how EST-based nuclear resources can be used to more fully resolve the phylogenetic history of species radiations.