Evolutionary analysis of Pinus densata Masters, a putative Tertiary hybrid : 1. Allozyme variation

Genomic data reveal cryptic lineage diversification and introgression in Californian golden cup oaks (section Protobalanus)

Here we study hybridization, introgression and lineage diversification in the widely distributed canyon live oak (Quercus chrysolepis) and the relict island oak (Q. tomentella), two Californian golden cup oaks with an intriguing biogeographical history. We employed restriction-site-associated DNA sequencing and integrated phylogenomic and population genomic analyses to study hybridization and reconstruct the evolutionary past of these taxa. Our analyses revealed the presence of two cryptic lineages within Q. chrysolepis. One of these lineages shares its most recent common ancestor with Q. tomentella, supporting the paraphyly of Q. chrysolepis. The split of these lineages was estimated to take place during the late Pliocene or the early Pleistocene, a time corresponding well with the common presence of Q. tomentella in the fossil records of continental California. Analyses also revealed historical hybridization among lineages, high introgression from Q. tomentella into Q. chrysolepis in their current area of sympatry, and widespread admixture between the two lineages of Q. chrysolepis in contact zones. Our results support that the two lineages of Q. chrysolepis behave as a single functional species phenotypically and ecologically well differentiated from Q. tomentella, a situation that can be only accommodated considering hybridization and speciation as a continuum with diffuse limits.

Demography and speciation history of the homoploid hybrid pine Pinus densata on the Tibetan Plateau

Pinus densata is an ecologically successful homoploid hybrid that inhabits vast areas of heterogeneous terrain on the south-eastern Tibetan Plateau as a result of multiple waves of colonization. Its region of origin, route of colonization onto the plateau and the directions of introgression with its parental species have previously been defined, but little is known about the isolation and divergence history of its populations. In this study, we surveyed nucleotide polymorphism over eight nuclear loci in 19 representative populations of P. densata and its parental species. Using this information and coalescence simulations, we assessed the historical changes in its population size, gene flow and divergence in time and space. The results indicate a late Miocene origin for P. densata associated with the recent uplift of south-eastern Tibet. The subsequent differentiation between geographical regions of this species began in the late Pliocene and was induced by regional topographical changes and Pleistocene glaciations. The ancestral P. densata population had a large effective population size but the central and western populations were established by limited founders, suggesting that there were severe bottlenecks during the westward migration out of the ancestral hybrid zone. After separating from their ancestral populations, population expansion occurred in all geographical regions especially in the western range. Gene flow in P. densata was restricted to geographically neighbouring populations, resulting in significant differentiation between regional groups. The new information on the divergence and demographic history of P. densata reported herein enhances our understanding of its speciation process on the Tibetan Plateau.

Genetic divergence, range expansion and possible homoploid hybrid speciation among pine species in Northeast China

Although homoploid hybrid speciation in plants is probably more common than previously realized, there are few well-documented cases of homoploid hybrid origin in conifers. We examined genetic divergence between two currently widespread pines in Northeast China, Pinus sylvestris var. mongolica and Pinus densiflora, and also whether two narrowly distributed pines in the same region, Pinus funebris and Pinus takahasii, might have originated from the two widespread species by homoploid hybrid speciation. Our results, based on population genetic analysis of chloroplast (cp), mitochondrial (mt) DNA, and nuclear gene sequence variation, showed that the two widespread species were divergent for both cp- and mtDNA variation, and also for haplotype variation at two of eight nuclear gene loci surveyed. Our analysis further indicated that P. sylvestris var. mongolica and P. densiflora remained allopatric during the most severe Quaternary glacial period that occurred in Northeast China, but subsequently exhibited rapid range expansions. P. funebris and P. takahasii, were found to contain a mixture of chlorotypes and nuclear haplotypes that distinguish P. sylvestris var. mongolica and P. densiflora, in support of the hypothesis that they possibly originated via homoploid hybrid speciation following secondary contact and hybridization between P. sylvestris var. mongolica and P. densiflora.

Tracing the recombination and colonization history of hybrid species in space and time

Hybrid speciation has long fascinated evolutionary biologists and laymen alike, presumably because it challenges our classical view of evolution as a 'one-way street' leading to strictly tree-like patterns of ancestry and descent. Homoploid hybrid speciation (HHS) has been a particularly interesting puzzle, as it appears to occur extremely rapidly, perhaps within less than 50 generations (McCarthy et al. 1995; Buerkle et al. 2000). Nevertheless, HHS may sometimes involve extended or repeated periods of recombination and gene exchange between populations subject to strong divergent natural selection (Buerkle & Rieseberg 2008). Thus, HHS provides a highly interesting setting for understanding the drivers and tempo of adaptive divergence and speciation in the face of gene flow (Arnold 2006; Rieseberg & Willis 2007; Nolte & Tautz 2009). In the present issue of Molecular Ecology, Wang et al. (2011) explore a particularly challenging issue connected to HHS: they attempt to trace the colonization and recombination history of an ancient (several MYA) hybrid species, from admixture and recombination in the ancestral hybrid zone to subsequent range shifts triggered by tectonic events (uplift of the Tibetan plateau) and climatic shifts (Pleistocene ice ages). This work is important because it addresses key issues related to the origin of the standing genetic variation available for adaptive responses (e.g. to climate change) and speciation in temperate species, which are topics of great current interest (Rieseberg et al. 2003; Barrett & Schluter 2008; de Carvalho et al. 2010).

Cytoplasmic composition in Pinus densata and population establishment of the diploid hybrid pine

Sequence and restriction site analyses of the paternally inherited chloroplast rbcL gene and maternally inherited mitochondrial nad1 fragments from the same set of populations and individuals were used to investigate cytoplasmic composition and population establishment of Pinus densata, a diploid pine that originated through hybridization between P. tabuliformis and P. yunnanensis. Two variable sites and three chlorotypes (TT, TC and GC) were detected on the rbcL gene of the three pines. P. densata harboured the three chlorotypes, two of which (TT, GC) were characteristic of the parental species, respectively. The third chlorotype (TC) was distributed extensively in seven of the 10 P. densata populations analysed, and might represent a mutation type or have been derived from an extinct parent. The distribution of chlorotypes, together with that of mitotypes, indicated that significant founder effect and backcross happened during the population establishment of the hybrid pine. P. tabuliformis and P. yunnanensis had acted as both mother and father donors, i.e. bi-directional gene flow existed between the two parental species in the past. Population differentiation of P. densata is high, as detected from the cytoplasmic genomes: GST = 0.533 for cpDNA and GST = 0.905 for mtDNA. The differences in cytoplasmic composition among the hybrid populations suggest that the local populations have undergone different evolutionary histories.

Origin(s) of the diploid hybrid species Helianthus deserticola (Asteraceae)

Homoploid hybrid speciation has traditionally been considered a rare event, dependent on the establishment of both a novel, balanced genotype and reproductive isolating barriers between the new species and its progenitors. However, more recent studies have shown that synthetic hybrids converge toward the chromosomal structure of natural hybrids after only a few generations, suggesting that this phenomenon may be more frequent than previously assumed. Here, the possibility that the diploid hybrid species Helianthus deserticola arose from more than one hybrid speciation event was investigated using patterns of variation from cpDNA, 18 nuclear microsatellite loci, and population interfertility. Helianthus deserticola contains cpDNA haplotypes characteristic of both parental species, is polyphyletic with one parental species based on nine microsatellite loci, and has a high degree of interfertility among populations. The data are consistent with either a single origin followed by introgression with the parental species or multiple origins. Analysis of microsatellite variation places the origin of H. deserticola between 170 000 and 63 000 years before present, making it unlikely that anthropogenic disturbances influenced its origin. Finally, the hybrid species generally has lower levels of genetic diversity but higher levels of differentiation among populations than either parental species.

Maternal lineages of Pinus densata, a diploid hybrid

Previous morphological, allozyme and chloroplast DNA data have suggested that Pinus densata originated through hybridization between P. tabuliformis and P. yunnanensis. In the present study, sequence and restriction site analyses of maternally inherited mitochondrial nad1 intron were used to detect variation patterns in 19 populations of P. tabuliformis, P. yunnanensis and P. densata. A total of three mitotypes (A, B, C) were detected. All but one of the populations of P. yunnanensis possessed mitotype B while all populations of P. tabuliformis had mitotype A. Pinus densata populations, on the other hand, harboured both mitotypes A and B, which are characteristic of P. tabuliformis and P. yunnanensis, respectively. This result gives strong additional evidence supporting the hybrid origin of this diploid pine. The distribution of mitotypes indicated very different mating compositions and evolutionary history among P. densata populations. It seems that local founder populations and backcrosses may have played important roles in the early establishment of P. densata populations. The uplift of the Tibetan Plateau had a significant impact on the distribution of maternal lineages of P. densata populations.

Genetic composition and diploid hybrid speciation of a high mountain pine, Pinus densata, native to the Tibetan plateau

Pinus densata has been suggested to have originated from hybridization events involving P. tabulaeformis and P. yunnanensis. In this study, allozyme differentiation at 12 loci was studied in 14 populations of P. tabulaeformis, P. densata, and P. yunnanensis from China. The observed genetic composition of P. densata supported the hybrid hypothesis and showed varying degrees of contribution from P. yunnanensis and P. tabulaeformis among its populations. These data, together with previous chloroplast DNA results, indicated different evolutionary histories among P. densata populations. To examine the possibility of ongoing hybridization among the three species, we analyzed patterns of linkage disequilibria between allozyme loci in ovule, pollen, and zygote pools. None of these tests suggested that there is significant ongoing gene exchange, implying that populations of P. densata have a stabilized hybrid nature. The normal fertility and high fecundity of P. densata indicate that this hybrid is maintained through sexual reproduction. P. densata represents an example of diploid hybrid speciation in an extreme ecological habitat that is both spatially and ecologically separated from that of its parents.

Genetic diversity and phylogenetic relatedness among six endemic Pterostylis species (Orchidaceae; series Grandiflorae) of Western Australia, as revealed by allozyme polymorphisms

Starch gel electrophoresis was employed to survey the allozyme polymorphism and phylogenetic relationships among 35 populations covering six closely related Western Australian endemic Pterostylis species (series Grandiflorae); viz P. rogersii, P. aspera, P. angusta, P. hamiltonii, P. scabra and P. aff. alata. The aim of this study was to determine intraspecific and interspecific genetic diversity and species relationships based on allozyme analysis. The frequencies of 56 alleles at 12 enzyme systems coded by 15 loci were determined along with a mean intraspecific genetic identity value. Allozyme markers clearly discriminated populations belonging to different species. Nei's genetic distance/identity co-efficient was used to measure the level of genetic differentiation among populations and species. Based on these values, a dendrogram was constructed which revealed that all the populations clustered into groups corresponding to the respective species. Gene diversity analysis among all the species revealed total genetic diversity H(t) of 0.23 with co-efficient of gene differentiation 10% (G(st)=0.10). Mean genetic variability (H(e)=0.136, P=40%) was also higher than for other outbreeding plant species. Mean genetic identity coefficient of populations of all species was 0.859 which increased to 0.877 upon exclusion of P. aff. alata, indicating a high degree of similarity among all species except P. aff. alata which segregated distinctively from the rest. Overall, the investigation provided independent support for the morphological segregation of these taxa.

Hybridization of Bird Species

Hybridization, the interbreeding of species, provides favorable conditions for major and rapid evolution to occur. In birds it is widespread. Approximately one in ten species is known to hybridize, and the true global incidence is likely to be much higher. A longitudinal study of Darwin's finch populations on a Galápagos island shows that hybrids exhibit higher fitness than the parental species over several years. Hybrids may be at an occasional disadvantage for ecological rather than genetic reasons in this climatically fluctuating environment. Hybridization presents challenges to the reconstruction of phylogenies, formulation of biological species concepts and definitions, and the practice of biological conservation.

Evolutionary analysis of Pinus densata (Masters), a putative Tertiary hybrid. : 2. A study using species-specific chloroplast DNA markers

Restriction fragment analysis and heterologous hybridization of chloroplast (cp) DNA was used to develop species-specific markers for P. tabulaeformis, P. yunnanensis and P. massoniana. Fragment patterns created by the BclI and DraI restriction enzymes and hybridization patterns to the psbC and psbD probes were distinctive among the three species. No intraspecific variation was detected with respect to any of the cpDNA markers developed in this study. The cpDNA markers obtained were subsequently used to examine the parentage of P. densata, a putative Tertiary hybrid between P. tabulaeformis and P. yunnanensis. The analysis demonstrated for the first time that P. densata populations accommodate chloroplast genomes of P. tabulaeformis and P. yunnanensis, which strongly supports earlier suggestions of the hybrid origin of this species. It appears that P. densata represents a stabilized natural hybrid that has become adapted to high mountain environments where neither of the parental species can normally grow.