Adaptation to replicate environments is often achieved through similar phenotypic solutions. Whether selection also produces convergent genomic changes in these situations remains largely unknown. The variable groundsel, Senecio lautus, is an excellent system to investigate the genetic underpinnings of convergent evolution, because morphologically similar forms of these plants have adapted to the same environments along the coast of Australia. We compared range-wide patterns of genomic divergence in natural populations of this plant and searched for regions putatively affected by natural selection. Our results indicate that environmental adaptation followed complex genetic trajectories, affecting multiple loci, implying both the parallel recruitment of the same alleles and the divergence of completely different genomic regions across geography. An analysis of the biological functions of candidate genes suggests that adaptation to coastal environments may have occurred through the recruitment of different genes participating in similar processes. The relatively low genetic convergence that characterizes the parallel evolution of S. lautus forms suggests that evolution is more constrained at higher levels of biological organization.

Storage roots of cassava (Manihot esculenta Crantz) exhibit a rapid post-harvest physiological deterioration (PPD) response that can occur within 24-72 h of harvest. PPD is an enzymatically mediated oxidative process with parallels to plant wound, senescence and defence responses. To characterise those genes that show significant change in expression during the PPD response we have used cDNA microarray technology to carry out a large-scale analysis of the cassava root transcriptome during the post-harvest period. We identified 72 non-redundant expressed sequence tags which showed altered regulation during the post-harvest period. Of these 63 were induced, whilst 9 were down-regulated. RNA blot analysis of selected genes was used to verify and extend the microarray data. Additional microarray hybridisation experiments allowed the identification of 21 root-specific and 24 root-wounding-specific sequences. Many of the up-regulated and PPD-specific expressed sequence tags were predicted to play a role in cellular processes including reactive oxygen species turnover, cell wall repair, programmed cell death, ion, water or metabolite transport, signal transduction or perception, stress response, metabolism and biosynthesis, and activation of protein synthesis.

Apomixis, asexual reproduction through seed, enables breeders to identify and faithfully propagate superior heterozygous genotypes by seed without the disadvantages of vegetative propagation or the expense and complexity of hybrid seed production. The availability of new tools such as genotyping by sequencing and bioinformatics pipelines for species lacking reference genomes now makes the construction of dense maps possible in apomictic species, despite complications including polyploidy, multisomic inheritance, self-incompatibility, and high levels of heterozygosity. In this study, we developed saturated linkage maps for the maternal and paternal genomes of an interspecific Brachiaria ruziziensis (R. Germ. and C. M. Evrard) × B. decumbens Stapf. F1 mapping population in order to identify markers linked to apomixis. High-resolution molecular karyotyping and comparative genomics with Setaria italica (L.) P. Beauv provided conclusive evidence for segmental allopolyploidy in B. decumbens, with strong preferential pairing of homologs across the genome and multisomic segregation relatively more common in chromosome 8. The apospory-specific genomic region (ASGR) was mapped to a region of reduced recombination on B. decumbens chromosome 5. The Pennisetum squamulatum (L.) R.Br. PsASGR-BABY BOOM-like (psASGR–BBML)-specific primer pair p779/p780 was in perfect linkage with the ASGR in the F1 mapping population and diagnostic for reproductive mode in a diversity panel of known sexual and apomict Brachiaria (Trin.) Griseb. and P. maximum Jacq. germplasm accessions and cultivars. These findings indicate that ASGR–BBML gene sequences are highly conserved across the Paniceae and add further support for the postulation of the ASGR–BBML as candidate genes for the apomictic function of parthenogenesis.

19Natural selection is a major driver for the origins of adaptations and new species 1 . Whether or 20 not the processes driving adaptation and speciation share a molecular basis remains largely 21 unknown 2 . Here, we show that divergence in hormone signalling contributed to the evolution 22 habits of S. lautus populations, therefore making evolution of the auxin pathway a natural 60 candidate to link the molecular basis of adaptation and speciation. We reasoned that if 61 divergence in the auxin pathway contributed to the evolution of adaptation and speciation in 62 S. lautus, we would discover the following evidence: First, we would detect similar patterns 63 of genetic divergence in auxin-related pathways across multiple erect and prostrate hybrid 64 and natural populations. Second, these populations would differ in phenotypes dependent on 65 auxin, such as their ability to alter the direction of growth in relation to gravity 10,16 . And third, 66 divergence in these auxin-dependent phenotypes would contribute to local adaptation and 67 intrinsic reproductive isolation between populations. 68We test these hypotheses primarily on coastal populations of S. lautus (Fig. 1a, Extended 69Data Table 1), which exhibit strong correlations between growth habit and the environments 70 they occupy 7 . Populations inhabiting sand dunes (Dune hereafter) are erect, while populations 71 growing on adjacent rocky headlands (Headland hereafter) are prostrate ( Fig. 1b). Erect and 72 prostrate growth habits can also be found in related populations from the alpine regions of 73 Australia, with a prostrate population inhabiting an exposed alpine meadow and an erect 74 population inhabiting a sheltered alpine gully (Fig. 1c). Dune populations are continually 75 exposed to high temperatures and sun radiation, low salinity, and low nutrient sand substrate, 76whereas Headland populations are exposed to high salinity, high nutrients and powerful 77 winds 17 . Neighbouring Dune and Headland populations are often sister taxa, group into two 78 major monophyletic clades (eastern and south-eastern) and have evolved their contrasting 79 growth habits independently multiple times 7,20 . These Dune and Headland populations are 80 locally adapted [17][18][19][20] and their F2 hybrids have low fitness 21 , indicating the presence of 81 intrinsic reproductive isolation. Furthermore, performing genetic, physiological, and 82 ecological experimental studies is achievable in this system due to its short life cycle, diploid 83 inheritance, and small vegetative size. Therefore, the Senecio lautus species complex 84The physiological basis of repeated evolution in S. lautus 126Considering we identified a multitude of different auxin related genes between erect and 127 prostrate populations of S. lautus and the regulation and transport of auxin is well established 128 to modulate gravitropism in plants, we predicted that these divergent growth habits may be a 129 direct consequence of changes in the auxin pathway, and can therefore contribute to 130 d...

The independent and repeated adaptation of populations to similar environments often results in the evolution of similar forms. This phenomenon creates a strong correlation between phenotype and environment and is referred to as parallel evolution. However, we are still largely unaware of the dynamics of parallel evolution, as well as the interplay between phenotype and genotype within natural systems. Here, we examined phenotypic and genotypic parallel evolution in multiple parapatric Dune-Headland coastal ecotypes of an Australian wildflower, Senecio lautus. We observed a clear trait-environment association in the system, with all replicate populations having evolved along the same phenotypic evolutionary trajectory. Similar phenotypes have arisen via mutational changes occurring in different genes, although many share the same biological functions. Our results shed light on how replicated adaptation manifests at the phenotypic and genotypic levels within populations, and highlight S. lautus as one of the most striking cases of phenotypic parallel evolution in nature.