A chemical perspective on the evolution of variation in Eucalyptus globulus

It is becoming increasingly easy to generate genotypic data but much harder to gather an equivalent amount of phenotypic information, particularly for chemical traits. In this study of Eucalyptus globulus ssp. globulus, we measured about 60 chemical leaf traits of trees growing in a common garden to address the following questions: (1) how much variation is there between geographic regions, populations within regions and within populations? (2) How do chemical traits vary over the species’ geographic range? (3) If so, does E. globulus ssp. globulus exhibit distinct chemotypes – plants that are morphologically similar but which differ chemically? (4) Are the affinities between E. globulus ssp. globulus and closely related subspecies apparent in the chemical variation? Variation among trees within populations contributed most variation in leaf chemistry followed by variation between geographic regions. For many traits, variation among populations within proposed races and variation among proposed races within geographic regions explained little of the total variation. There was a cline in the concentration of secondary chemicals with the lowest concentrations in Tasmanian populations and the highest in those from eastern Victoria, with intermediate concentrations in populations from Bass Strait Islands. We identified three chemotypes, characterised by specific terpenes and formylated phloroglucinol compounds. The frequency of occurrence of these chemotypes showed a geographic pattern also, with “chemotype 1” predominating in Tasmania, while “chemotypes 2 and 3” occurred at highest frequency in eastern Victoria. We suggest that the chemotypes reflect introgression between E. globulus ssp. globulus and the three closely related subspecies – E. globulus ssp. bicostata, E. globulus ssp. maidenii and E. globulus ssp. pseudoglobulus. Although the formation of land-bridges with fluctuating sea levels has no doubt shaped the evolutionary history of all four subspecies, we propose that the migratory swift parrot (Lathamus discolor), an important pollinator and a species closely associated with E. globulus, has helped shape the evolution of the four tree subspecies.     

Development of SCAR molecular markers for early and late differentiation of Eucalyptus globulus ssp globulus from E. globulus ssp maidenii

The genus Eucalyptus includes over 700 species, some of which are the most widely planted hardwoods worldwide. Each species and subspecies of Eucalyptus present different characteristics regarding its wood quality and yield. This fact makes it very important to work with known species/subspecies so as to optimize handling and conservation of forest resources. Some of them are morphologically very similar, making it difficult to differentiate by simple observation. This is the case with Euclyptus globulus ssp globulus and E. globulus ssp maidenii, which can only be distinguished in the adult tree. These issues can be avoided using well-characterized seeds. This can be quite expensive, especially for the small growers. An alternative approach is to develop simple methods for the differentiation of the two subspecies. In this work, we develop a quick method, based on SCAR molecular markers derived from RAPD molecular markers, for the differentiation of the subspecies of E. globulus, in particular E. globulus ssp globulus and E. globulus ssp maidenii.     

GENETIC DIFFERENTIATION,SYMPATRIC SPECIATION,AND THE ORIGIN OF A DIPLOID SPECIES OF STEPHANOMERIA

Evidence is presented that a geographically peripheral population of the annual Stephanomcria exigua ssp. coronaria (Compositae), a widespread and ecologically diverse species, has recently given rise by a process of sympatric speciation to a diploid species presently designated “Malheurensis.” The new species comprises less than 250 individuals and is found only at a single locality in eastern Oregon where it grows interspersed with its parental population. Stephanomeria exigua ssp. coronaria is an obligate outcrosser and “Malheurensis” is highly self-pollinating. Reproductive isolation is maintained by differences in breeding system, a crossability barrier that reduces seed set following cross-pollination between them, and reduction in hybrid fertility caused by chromosomal structural differences. They are very similar morphologically. Electrophoretic analyses of seven enzyme systems demonstrate that all the alleles but one at the controlling 13 gene loci in “Malheurensis” are identical to alleles in ssp. coronaria. The new species displays certain maladapted features including loss of the specific requirements for seed germination characteristic of the progenitor population of ssp. coronaria. The origin of “Malheurensis” appears to be an exception to the theory of geographical speciation because spatial isolation is not necessary at any time for the origin or establishment of its reproductive isolating barriers. The nature of these barriers plus the genetic homogeneity of the species are compatible with the hypothesis that it derives from a single progenitor individual. Very little genetic change is involved initially in this mode of speciation.     

A comparative analysis of population structure of a forest tree, Eucalyptus globulus (Myrtaceae), using microsatellite markers and quantitative traits

Eucalyptus globulus (Myrtaceae) is a forest tree native to southeastern Australia, but is grown globally for pulpwood and timber. Eight microsatellite loci were used to determine the degree of selectively neutral differentiation between native populations of the geographic races of E. globulus that are used in a national breeding programme. Spatial differentiation was detected among 340 samples from across the species range (F _ST=0.09±0.02). Analysis of molecular variance showed that there was significant variation between the races, and an unweighted pair group method with arithmetic mean analysis of Nei’s genetic distance between races showed that geographically proximal races tended to be more closely related than geographically distant races. This contrasted markedly with analyses based on quantitative genetic data, where some races appeared to be highly divergent from their geographically closest neighbours. Comparison of racial differentiation based on quantitative (Q _ST) and molecular (F _ST) data suggested that at least five of the quantitative traits used for defining races of E. globulus have been influenced by natural selection, resulting in cases of both phenotypic divergence of parapatric races and phenotypic convergence of allopatric races. We conclude that selectively neutral molecular markers are more useful than quantitative genetic data for identifying the evolutionary affinities and lineages within E. globulus. However, both sources of information should be used in defining evolutionarily important units for conservation. The population structure observed in E. globulus has important consequences for future association studies and may also affect breeding strategies if significant genome co-adaptation has occurred.     

GENETIC RELATIONSHIPS AND PATTERNS OF ALLOZYMIC DIVERGENCE IN THE IPOMOPSIS AGGREGATA COMPLEX AND RELATED SPECIES (POLEMONIACEAE)

The Ipomopsis aggregata complex consists of diploid, outcrossing, perennial herbs. The group is highly variable morphologically and is treated as three species: I. aggregata, I. tenuituba, and I. arizonica. Geographic races of I. aggregata and I. tenuituba are recognized as subspecies. Enzyme electrophoresis was used to examine genetic relationships among populations and taxa in the Ipomopsis aggregata complex and some related species. Genetic data for 23 allozyme loci from 60 populations were also used to determine how genetic variation is distributed geographically. Populations in the southwestern United States were more variable than those in the northwest: the center of genetic diversity corresponded to the center of species diversity. Allozymic data provided no evidence of loss of genetic variability associated with recent and rapid divergence. Genetic relationships based on Nei's genetic identity did not correspond to taxonomic relationships. For example, populations of both I. arizonica and I. tenuituba clustered within I. aggregata. Despite relatively high levels of genetic diversity among populations, diversity among taxa was low. Results indicated that floral divergence and concomitant speciation have occurred recently in the Ipomopsis aggregata complex. Allozymic patterns also reflected convergent evolution for floral morphology and possible introgression. Despite morphological differences among species, insufficient evolutionary time has elapsed for allelic fixation at neutral or near-neutral allozyme loci.     

A footprint of tree‐genetics on the biota of the forest floor

Understanding how far the effects of genes extend beyond the phenotype of an individual or population, is fundamental to the developing field of community genetics. We therefore assessed two geographically and genetically distinct populations of the Australian forest tree, Eucalyptusglobulus, and the existence of genetic effects on a leaf litter invertebrate community and soil characteristics within a 15 year old common garden. Twenty trees per population were randomly selected for felling and placement of the apical branch next to the stump. This produced a leaf litter habitat of known genotype. Pitfall trap sampling for invertebrates, and linseed bioassay analyses of soil, were conducted within this habitat. Two key findings emerged. Firstly, assessment of 27 invertebrate orders (57 924 individuals) revealed significant population‐level variation in leaf litter biodiversity (i.e. in community richness, abundance, composition and beta diversity). Secondly, considerable population‐level differences in soil characteristics were evident based on linseed germination and growth responses. While recent findings in E. globulus have demonstrated consequences of genetic variation within forest trees for organisms that interact directly (i.e. proximally) with the living tree, these findings highlight the distal impacts that intraspecific genetic variation may have on communities and ecosystems. Such community genetic considerations have important implications for in situ community conservation, biodiversity management within restoration and plantation forestry, and our understanding of community‐level evolutionary interactions involving foundation species.     

Conservation genetics of the loggerhead shrike (Lanius ludovicianus) in central and eastern North America

This study examines geneticstructure of central and eastern North American Loggerhead Shrike (Lanius ludovicianus)populations. Samples derived from 27populations (n = 206) covering the range of threerecognized subspecies: L. l. migrans,L. l. ludovicianus, and L. l.excubitorides, and included locales from aputative intergrade zone between twosubspecies. For L. l. migrans, samplesinclude both those from extant populations andfrom museum specimens spanning approximately130 years. For all samples we obtained 267 basepairs of mitochondrial control region sequenceand identified a total of 23 distincthaplotypes. For a subset of samplesrepresenting a locale centered on the Canadianportion of an intergrade zone between migrans and excubitorides and locales onalternate sides of the intergrade, we obtainedadditional sequence for an intron of thenuclear glyceraldehyde-3-phosphatedehydrogenase gene. Analyses of temporal trendsin control region diversity of L. l.migrans populations indicate a diminutioncoincident with the decline in populationnumbers. Results from an Analysis of MolecularVariance on the control region data showed thata significant amount of total control regionspatial variation was apportioned among thethree subspecies (24.42%; P < 0.01). Furtheranalyses indicated statistically significantdifferences between eastern and westernpopulations of L. l. migrans. We found nosignificant differences among consideredpopulations in frequencies of six identifiedGpdh alleles, although this result ispreliminary because of small sample sizes.However, both the mitochondrial and intron datasuggest a higher genetic diversity in theintergrade zone. Based on our analyses wedefine four management units for eastern andcentral populations of Loggerhead Shrikes.     

Patterns of allozyme variation in western Eurasian Fagus

Fagus sylvatica L. is one of the most widespread broad‐leaved trees in the temperate forests of the northern hemisphere. In addition to two subspecies, F. sylvatica ssp. sylvatica in Europe and F. sylvatica ssp. orientalis in south‐western Asia, two further taxa were described: F. moesiaca (Maly) Czeczott in the south‐western Balkans and F. taurica Popl. in Crimea. The opinions about the number and ranks of taxa within this complex are highly controversial. To assess the degree of genetic differentiation among them, and to reveal geographical patterns of genetic diversity and their relationships to history and biogeography of beech populations, genetic variation at 12 allozyme loci was studied in 279 populations in western Eurasia. A Bayesian analysis of population structure revealed the existence of two clusters, which fairly well coincided with F. sylvatica ssp. sylvatica and F. sylvatica ssp. orientalis, whereby the populations from the south‐western Balkans and Crimea contained a mixture of these two gene pools. On the other hand, a neighbour‐joining tree based on pairwise F_ST failed to separate the subspecies into well‐defined distinct clades. Populations of F. sylvatica ssp. orientalis proved to be incomparably more differentiated than ssp. sylvatica (F_ST = 0.157 and 0.032, respectively). Asian populations also showed higher levels of allelic richness both on population and taxon levels than the European ones (the number of alleles after rarefaction was 3.40 and 4.27 in F. sylvatica ssp. sylvatica and ssp. orientalis, respectively). This indicates that the gene pool of F. sylvatica ssp. orientalis has not been depleted by reduced population sizes during the Pleistocene glaciations, as is the case of F. sylvatica ssp. sylvatica. Genetic similarities between isolated regional populations are explained by shared ancestral polymorphisms and/or range overlaps with subsequent hybridization in the past. © 2007 The Linnean Society of London, Botanical Journal of the Linnean Society, 2007, 154 , 165–174.     

MORPHOLOGICAL VARIATION WITHIN AND BETWEEN NATURAL POPULATIONS OF NON-TIDE POOL FUCUS DISTICHUS (PHAEOPHYTA) IN NEW ENGLAND1,2

The sources of morphological variation in natural populations of Fucus distichus L. ssp. edentatus (De la Pyiaie) Powell and F. distichus L. ssp, evanescens (C. Agardh) Powell from New England were evaluated. Individuals from different populations were morphologically distinct as judged by population means and analysis of variance. A correlation between the plant's form and its habitat was established by field observation. The broadest material grows in calm estuarine habitats, while the narrowest plants occur in exposed, open coastal areas. Major differences in morphology also appear seasonally. In addition, microhabitat factors such as exposure to wave action and elevation explain some morphological variation. Cultured germlings from distinct populations of “evanescens” and “edentatus” type plants were outplanted to an experimental garden in order to ascertain whether the variation was heritable or environmentally induced. The latter experiments indicate that major differences in morphology are genetically determined.     

Estimating population boundaries using regional and local-scale spatial genetic structure: an example in Eucalyptus globulus

Eucalyptus globulus Labill is a foundation tree species over its disjunct distribution in southeastern Australia. The quality of its pulp makes it the most important hardwood species in the world. The importance of E. globulus prompted the establishment of common gardens from seed collected across its geographic range. This enabled us to study the genetic structure of the species, its population boundaries, and gene flow using 444 trees from different open-pollinated families that were genotyped at 16 microsatellite loci. A Bayesian clustering method was used to resolve five genetically distinct groups across the geographical range. These groups were identified as regions, which varied in diameter from 38 to 294?km and contain 4 to 16 putative populations. For two of these regional groups, we used spatial autocorrelation analysis based on assignment of trees to their natural stands to examine gene flow within each region. Consistent significant local-scale spatial structure occurred in both regions. Pairs of individuals within a region showed significant genetic similarity that extended beyond 40?km, suggesting distant movement of pollen. This suggests that breeding populations in E. globulus are much bigger than traditionally accepted in eucalypts. Our results are important for the management of genetic diversity and breeding populations in E. globulus. Similar studies of a variety of eucalypts pollinated by insects and birds will determine whether the local-scale genetic structure of E. globulus is unusual.     

Unexpected hybridization reveals the utility of genetics in native plant restoration

Native plant materials (NPMs) are increasingly utilized during the restoration of disturbed plant communities. Here, we analyze next‐generation genetic sequencing data for Hilaria jamesii, a dominant graminoid across drylands of the southwestern United States, and document that the species' only commercially‐available NPM, “Viva,” is a hybrid between H. jamesii and its sister species, Hilaria mutica. In fact, hybrids between these species are common where they geographically overlap. Furthermore, we show that the “Viva” hybrid has successfully been moved beyond the hybrid zone and into the core range of H. jamesii. The potential ramifications of introducing novel genetic material into H. jamesii are discussed, as well as the utility of genetic analyses to protect species' natural patterns of genetic diversity and help managers make informed decisions regarding the development and deployment of NPMs.     

Recurrent nuclear DNA introgression accompanies chloroplast DNA exchange between two eucalypt species

Numerous studies within plant genera have found geographically structured sharing of chloroplast (cp) DNA among sympatric species, consistent with introgressive hybridization. Current research is aimed at understanding the extent, direction and significance of nuclear (nr) DNA exchange that accompanies putative cpDNA exchange. Eucalyptus is a complex tree genus for which cpDNA sharing has been established between multiple species. Prior phylogeographic analysis has indicated cpDNA introgression into the widespread forest species Eucalyptus globulus from its rare congener E. cordata. In this study, we use AFLP markers to characterize corresponding nrDNA introgression, on both a broad and fine spatial scale. Using 388 samples we examine (i) the fine‐scale spatial structure of cp and nrDNA introgression from E. cordata into E. globulus at a site in natural forest and (ii) broad‐scale patterns of AFLP marker introgression at six additional mixed populations. We show that while E. globulus and E. cordata retain strongly differentiated nuclear gene pools overall, leakage of nrDNA occurs at mixed populations, with some AFLP markers being transferred to E. globulus recurrently at different sites. On the fine scale, different AFLP fragments show varying distances of introgression into E. globulus, while introgression of cpDNA is extensive. The frequency of E. cordata markers in E. globulus is correlated with spatial proximity to E. cordata, but departs from expectations based on AFLP marker frequency in E. cordata, indicating that selection may be governing the persistence of introgressed fragments in E. globulus.     

Genetic differentiation of metallicolous and non-metallicolous Armeria maritima (Mill.) Willd. taxa (Plumbaginaceae) in Central Europe

This study investigates the genetic differentiation within the Central European Armeria maritima (Mill.) Willd. complex with special reference to the metallicolous populations using AFLP markers. Our sampling comprised all metallicolous (ssp. halleri, hornburgensis, bottendorfensis, eifeliaca, calaminaria), and non-metallicolous taxa (ssp. maritima, elongata, alpina). Geographical and genetic distances between populations were moderately positively correlated. Genetic variability of metallicolous and non-metallicolous populations was not significantly different. Lowland populations were clearly differentiated from the alpine populations. Within the lowland group metallicolous and non-metallicolous populations were not genetically differentiated. All lowland populations show a regional differentiation and close relationships to ssp. elongata. Thus, the metallicolous taxa should not be maintained as subspecies. Likewise, their treatment as varieties of a ssp. halleri s.l. is critical because this taxon cannot be consistently characterized throughout its geographical range and may be an artefact itself. If a taxonomical recognition should be considered necessary it is advisable to treat the microendemics as varieties of ssp. elongata.     

Analysis of the genetic diversity and relationships among and within species of Hippophae (Elaeagnaceae) based on RAPD markers

RAPD markers were used to assess the genetic diversity and inter- and intra-specific relationships of the genus Hippophae L. and to study the correlation between genetic distances and geographic distances among populations of H. rhamnoides ssp. sinensis. The results analyzed by the percentage of polymorphic loci and Shannon information index indicated that a high level of genetic diversity existed both among and within species of the genus Hippophae. In the UPGMA dendrogram, the species or subspecies were clustered into two main groups but not strictly grouped according to sect. Hippophae and sect. Gyantsensis Lian. The multiple regression analysis and Mantel test both indicated a significant correlation between genetic distance and altitude distance among populations of H. rhamnoides ssp. sinensis, and the cluster analysis suggested that the genetic variation among populations of H. rhamnoides ssp. sinensis was linked to their monophyletic origin. Moreover, some degree of genetic differentiation was found among samples collected at different times.     

Molecular and morphological divergence in a stygobiont gastropod lineage (Truncatelloidea,Moitessieriidae, Paladilhiopsis) within an isolated karstic area in the Mecsek Mountains (Hungary)

Truncatelloid gastropods are one of the most species‐rich subterranean invertebrate groups. Their current taxonomy is based on morphological characters. However, this is not a comprehensive approach and does not take into account the degree of phylogenetic divergence between stygobiont populations inhabiting hydrologically isolated but geographically close caves. We studied two Paladilhiopsis populations of a small and isolated karstic area (Mecsek Mountains, Hungary) with two hydrologically separated cave systems, investigating morphological (shell morphometrics) and genetic (COI, 16S) divergence together. The populations differed both morphologically and genetically: we found strong divergence in the relative width of the shell (best described by the variable “shell angle”) and a 6.4% divergence in COI. This provides strong support for the presence of two distinct taxa; however, it is still doubtful whether they differ at the species or the subspecies level. In one of the caves, we found representatives of both haplotypes (and phenotypes), which can be explained by secondary contact after an allopatric divergence.     

Genetic structure and differentiation of Plantago major reveals a pair of sympatric sister species

Seeds of the widespread weed Plantago major were collected from 10 European countries, as well as Trinidad and North America. The seed collections were from populations of two taxa which are ecologically rather than geographically separated and formally recognized as the subspecies Plantago major ssp. major and P.m. ssp. intermedia (also called P.m. ssp. pleiosperma). Eight polymorphic allozyme loci and 73 random-primed DNA fragments were scored, as well as 11 morphological characters. Complete concordance between morphological traits and genetic data provides evidence that these two taxa, although very similar, are distinct species. They are both widespread, they are broadly sympatric and capable of interbreeding. However, slight morphological and ecological differences coincide with genetic clustering of populations from widely separated locations. In addition, P. major and P. intermedia differ in their population structure: P. intermedia has greater genetic diversity among populations and less genetic variance within populations than P. major. We suggest that differences between the two species in their levels of selfing may explain the distinctive genetic structure of each species. We hypothesize a link between selfing rate and lifespan of the two taxa. P. major is characterized by lower genetic variation among populations, a higher rate of outcrossing, longer lifespan and production of fewer seeds per seed capsule. P. intermedia is more highly structured with much differentiation among populations, a higher rate of inbreeding and it often grows as an annual.     

The biogeography and genetic relationships of Juniperus oxycedrus and related taxa from the Mediterranean and Macaronesian regions

Despite Juniperus spp. being an important component of Mediterranean arid and semi‐arid ecosystems, there is a lack of complex studies on their biogeographical patterns. Using 16 morphological cone and seed traits and three nuclear microsatellite markers, we investigated the morphological and genetic variability of seven Mediterranean and Macaronesian Juniperus taxa (J. oxycedrus ssp. oxycedrus, J. oxycedrus ssp. badia, J. brevifolia, J. cedrus, J. deltoides, J. macrocarpa and J. navicularis) to identify biogeographical trends and interspecific genetic relationships. The highest gene diversity was measured in J. oxycedrus ssp. oxycedrus (H_E = 0.716) and the lowest in J. brevifolia (H_E = 0.441). The west Mediterranean was characterized by a higher level of genetic diversity than the east Mediterranean. A lack of significant genetic differences between European and African populations of J. oxycedrus suggests that the Strait of Gibraltar was not a significant barrier to gene flow, but has promoted some morphological differentiation. The genetic and morphological results strongly support the recognition of J. macrocarpa, J. navicularis and J. deltoides at the species rank, whereas J. oxycedrus ssp. badia should be included in J. oxycedrus. © 2014 The Linnean Society of London, Botanical Journal of the Linnean Society, 2014, 174 , 637–653.     

Conservation of genetic diversity hotspots of the high‐valued relic yellowhorn (Xanthoceras sorbifolium) considering climate change predictions

Genetic structure and major climate factors may contribute to the distribution of genetic diversity of a highly valued oil tree species Xanthoceras sorbifolium (yellowhorn). Long‐term over utilization along with climate change is affecting the viability of yellowhorn wild populations. To preserve the species known and unknown valuable gene pools, the identification of genetic diversity “hotspots” is a prerequisite for their consideration as in situ conservation high priority. Chloroplast DNA (cpDNA) diversity was high among 38 natural populations (H_d = 0.717, K = 4.616, Tajmas’ D = ?0.22) and characterized by high genetic divergence (F_ST = 0.765) and relatively low gene flow (N_m = 0.03), indicating populations isolation reflecting the species’ habitat fragmentation and inbreeding depression. Six out of the studied 38 populations are defined as genetic diversity “hotspots.” The number and geographic direction of cpDNA mutation steps supported the species southwest to northeast migration history. Climatic factors such as extreme minimum temperature over 30 years indicated that the identified genetic “hotspots” are expected to experience 5°C temperature increase in next following 50 years. The results identified vulnerable genetic diversity “hotspots” and provided fundamental information for the species’ future conservation and breeding activities under the anticipated climate change. More specifically, the role of breeding as a component of a gene resource management strategy aimed at fulfilling both utilization and conservation goals.