Speciation in the presence of gene flow: population genomics of closely related and diverging Eucalyptus species (original) (raw)
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Tree Genetics & Genomes, 2022
The evolutionary trajectory of a population both influences and is influenced by characteristics of its genome. A disjunct population, for example is likely to exhibit genomic features distinct from those of continuous populations, reflecting its specific evolutionary history and influencing future recombination outcomes. We examined genetic diversity, population differentiation and linkage disequilibrium (LD) across the highly disjunct native range of the Australian forest tree Eucalyptus globulus, using 203,337 SNPs genotyped in 136 trees spanning seven races. We found support for four broad genetic groups, with moderate F ST , high allelic diversity and genome-wide LD decaying to an r 2 of 0.2 within 4 kb on average. These results are broadly similar to those reported previously in Eucalyptus species and support the 'ring' model of migration proposed for E. globulus. However, two of the races (Otways and Southeastern Tasmania) exhibited a much slower decay of LD with physical distance than the others and were also the most differentiated and least diverse, which may reflect the effects of selective sweeps and/or genetic bottlenecks experienced in their evolutionary history. We also show that F ST and rates of LD vary within and between chromosomes across all races, suggestive of recombination outcomes influenced by genomic features, hybridization or selection. The results obtained from studying this species serve to illustrate the genomic effects of population disjunction and further contribute to the characterisation of genomes of woody genera.
Genetics, 2004
The genetic architecture of hybrid fitness characters can provide valuable insights into the nature and evolution of postzygotic reproductive barriers in diverged species. We determined the genome-wide distribution of barriers to introgression in an F 1 hybrid of two Eucalyptus tree species, Eucalyptus grandis (W. Hill ex Maiden.) and E. globulus (Labill.). Two interspecific backcross families (N ϭ 186) were used to construct comparative, single-tree, genetic linkage maps of an F 1 hybrid individual and two backcross parents. A total of 1354 testcross AFLP marker loci were evaluated in the three parental maps and a substantial proportion (27.7% average) exhibited transmission ratio distortion (␣ ϭ 0.05). The distorted markers were located in distinct regions of the parental maps and marker alleles within each region were all biased toward either of the two parental species. We used a Bayesian approach to estimate the position and effect of transmission ratio distorting loci (TRDLs) in the distorted regions of each parental linkage map. The relative viability of TRDL alleles ranged from 0.20 to 0.72. Contrary to expectation, heterospecific (donor) alleles of TRDLs were favored as often as recurrent alleles in both backcrosses, suggesting that positive and negative heterospecific interactions affect introgression rates in this wide interspecific pedigree. several hybrid populations ; Burke South Africa.
Molecular Phylogenetics …, 2011
A set of over 8000 Diversity Arrays Technology (DArT) markers was tested for its utility in high-resolution population and phylogenetic studies across a range of Eucalyptus taxa. Small-scale population studies of Eucalyptus camaldulensis, Eucalyptus cladocalyx, Eucalyptus globulus, Eucalyptus grandis, Eucalyptus nitens, Eucalyptus pilularis and Eucalyptus urophylla demonstrated the potential of genome-wide genotyping with DArT markers to differentiate species, to identify interspecific hybrids and to resolve biogeographic disjunctions within species. The population genetic studies resolved geographically partitioned clusters in E. camaldulensis, E. cladocalyx, E. globulus and E. urophylla that were congruent with previous molecular studies. A phylogenetic study of 94 eucalypt species provided results that were largely congruent with traditional taxonomy and ITS-based phylogenies, but provided more resolution within major clades than had been obtained previously. Ascertainment bias (the bias introduced in a phylogeny from using markers developed in a small sample of the taxa that are being studied) was not detected. DArT offers an unprecedented level of resolution for population genetic, phylogenetic and evolutionary studies across the full range of Eucalyptus species.
Forests, 2021
The recovery of genealogy in both natural and captive populations is critical for any decision in the management of genetic resources. It allows for the estimation of genetic parameters such as heritability and genetic correlations, as well as defining an optimal mating design that maintains a large effective population size. We utilised “genotyping-by-sequencing” (GBS) in combination with bioinformatics tools developed specifically for GBS data to recover genetic relatedness, with a focus on parent-offspring relationships in a Eucalyptus nitens breeding population as well as recognition of individuals representing other Eucalyptus species and putative hybrids. We found a clear advantage on using tools specifically designed for data of highly variable sequencing quality when recovering genetic relatedness. The parent-offspring relatedness showed a significant response to data filtering from 0.05 to 0.3 when the standard approach (G1) was used, while it oscillated around 0.4 when the...
Genetic diversity in the continuously distributed Eucalyptus marginata Donn ex Smith from southwestern Australia was investigated using nuclear RFLP loci. Diversity was assessed in 15 populations from across the range of E. marginata, including the three morphologically recognised subspecies, and one population of the closely related E. staeri. Moderate levels of genetic diversity (H T = 0.345) were detected in Eucalyptus marginata but there was little genetic structure and low differentiation between populations (θ = 0.034). Isolation by distance was observed, but there was differing influence of gene flow and drift over different spatial scales. There was no genetic support for the recognition of three subspecies, or the informal division of northern and southern forms recognised by foresters. Some populations showed a high fixation index most likely due to neighbourhood structure within populations. The lack of genetic structure and low population differentiation indicates that collection of germplasm for rehabilitation of forest sites following mining or Phythophthora cinnamomi infection, may be made at a regional scale.
Genetic Diversity Within and between Natural Populations of Eucalyptus occidentalis (Myrtaceae)
Silvae Genetica
Eucalyptus occidentalis is endemic to the south-west of Australia, occurring in small isolated populations in wet depressions and along drainage lines. The level of genetic diversity and pattern of structuring within and between populations was investigated using nuclear RFLP analysis of 10 populations. The level of genetic diversity was moderate and similar in the populations from the main range but lower in the outlier populations from the eastern end of the range. There was no evidence of inbreeding within the populations. The level of population differentiation was low but significantly different from zero, and the populations from the eastern end of the range showed higher levels of differentiation from each other and from the populations in the main range. The pattern of genetic diversity in E. occidentalis indicates historical connectivity between populations and the species was probably more abundant with a wider distribution in the past, except for the eastern end of the range where the species distribution appears to have always been fragmented. The pattern of population differentiation is similar to the pattern of differentiation in quantitative traits that has been observed in provenance trials. Sampling strategies for breeding programs should focus on the main range of the species.
2011
Eucalyptus obliqua L'Hér. is widespread across south-eastern Australia. On the island of Tasmania it has a moreor-less continuous distribution across its range and it dominates much of the wet sclerophyll forest managed for forestry purposes. To understand better the distribution of genetic variation in these native forests we examined nuclear microsatellite diversity in 432 mature individuals from 20 populations of E. obliqua across Tasmania, including populations from each end of three locally steep environmental gradients. In addition, chloroplast microsatellite loci were assessed in 297 individuals across 31 populations. Nuclear microsatellite diversity values in E. obliqua were high (average H E = 0.80) and inbreeding coefficients low (average F = 0.02) within these populations. The degree of differentiation between populations was very low (F ST = 0.015). No significant microsatellite differentiation could be found across three locally steep environmental gradients, even though there is significant genetic differentiation in quantitative traits. This suggests that the observed quantitative variation is maintained by natural selection. Population differentiation based on chloroplast haplotypes was high (G ST = 0.69) compared with that based on nuclear microsatellites, suggesting that pollen-mediated gene flow is >150 times the level of seed-mediated gene flow in this animal-pollinated species; hence, pollen is likely to be the main mode of gene flow countering selection along local environmental gradients. Implications of these results for silvicultural practices are discussed.
New Phytologist, 2016
Summary In order to contribute to evolutionary resilience and adaptive potential in highly modified landscapes, revegetated areas should ideally reflect levels of genetic diversity within and across natural stands. Landscape genomic analyses enable such diversity patterns to be characterized at genome and chromosomal levels. Landscape‐wide patterns of genomic diversity were assessed in Eucalyptus microcarpa, a dominant tree species widely used in revegetation in Southeastern Australia. Trees from small and large patches within large remnants, small isolated remnants and revegetation sites were assessed across the now highly fragmented distribution of this species using the DArTseq genomic approach. Genomic diversity was similar within all three types of remnant patches analysed, although often significantly but only slightly lower in revegetation sites compared with natural remnants. Differences in diversity between stand types varied across chromosomes. Genomic differentiation was ...
Unravelling the evolutionary history of Eucalyptus cordata (Myrtaceae) using molecular markers
2014
We studied the evolutionary processes shaping the genetic diversity in the naturally fragmented Eucalyptus cordata, a rare homoblastic tree endemic to the island of Tasmania. A genome-wide scan showed that E. cordata and the endangered heteroblastic E. morrisbyi were closely related, suggesting a neotenous origin of E. cordata from an endemic heteroblastic ancestor. Bayesian cluster analysis based on nuclear microsatellites assayed in 567 E. cordata and E. morrisbyi individuals revealed five genetic clusters. Two clusters comprised populations that correspond to putative ancestral gene pools linking E. cordata and E. morrisbyi. Another cluster included populations that transgressed the drowned Derwent River valley, suggestive of a wider glacial distribution. However, the majority of individuals occurred in the two genetic clusters distributed in the southwest and northeast of the range of E. cordata. The elevated genetic diversity in populations comprising these clusters suggests that they represent two recently fragmented cores of the distribution. Genetic evidence suggests that the newly described, localised E. cordata subspecies quadrangulosa has been recently selected from within the morphologically diverse, southwestern cluster. We argue that multiple phases of isolation and drift have led to the contemporary pattern of molecular variation and the scattering of relictual and more recently derived populations across the species distribution.