Evolutionary consequences of shifts to bird-pollination in the Australian pea-flowered legumes (Mirbelieae and Bossiaeeae)

BACKGROUND Interactions with pollinators are proposed to be one of the major drivers of diversity in angiosperms. Specialised interactions with pollinators can lead to specialised floral traits, which collectively are known as a pollination syndrome. While it is thought that specialisation to a pollinator can lead to either an increase in diversity or in some cases a dead end, it is not well understood how transitions among specialised pollinators contribute to changes in diversity. Here, we use evolutionary trait reconstruction of bee-pollination and bird-pollination syndromes in Australian egg-and-bacon peas (Mirbelieae and Bossiaeeae) to test whether transitions between pollination syndromes is correlated with changes in species diversity. We also test for directionality in transitions that might be caused by selection by pollinators or by an evolutionary ratchet in which reversals to the original pollination syndrome are not possible. RESULTS Trait reconstructions of Australian egg-and-bacon peas suggest that bee-pollination syndrome is the ancestral form and that there has been replicated evolution of bird-pollination syndromes. Reconstructions indicate potential reversals from bird- to bee-pollination syndromes but this is not consistent with morphology. Species diversity of bird-pollination syndrome clades is lower than that of their bee-pollination syndrome sisters.We estimated the earliest transitions from bee- to bird-pollination syndrome occurred between 30.8 Ma and 10.4 Ma. Geographical structuring of pollination syndromes was found; there were fewer bird-pollination species in the Australian southeast temperate region compared to other regions of Australia. CONCLUSIONS A consistent decrease in diversification rate coincident with switches to bird pollination might be explained if greater dispersal by bird pollinators results in higher levels of connectivity among populations and reduced chances of allopatric speciation.The earliest transitions overlap with the early diversification of Australian honeyeaters - the major lineage of pollinating birds in Australia. Our findings are consistent with the idea that environment and availability of pollinators are important in the evolution of pollination syndromes. Changes in flower traits as a result of transitions to bird-pollination syndrome might also limit reversals to a bee-pollination syndrome.Funding was provided by the Australian Research Council (grant number: DP0985473)

Australia's arid-adapted butcherbirds experienced range expansions during Pleistocene glacial maxima

A model of range expansions during glacial maxima (GM) for cold-adapted species is generally accepted for the Northern Hemisphere. Given that GM in Australia largely resulted in the expansion of arid zones, rather than glaciation, it could be expected that arid-adapted species might have had expanded ranges at GM, as cold-adapted species did in the Northern Hemisphere. For Australian biota, however, it remains paradigmatic that arid-adapted species contracted to refugia at GM. Here we use multilocus data and ecological niche models (ENMs) to test alternative GM models for butcherbirds. ENMs, mtDNA and estimates of nuclear introgression and past population sizes support a model of GM expansion in the arid-tolerant Grey Butcherbird that resulted in secondary contact with its close relative - the savanna-inhabiting Silver-backed Butcherbird - whose contemporary distribution is widely separated. Together, these data reject the universal use of a GM contraction model for Australia's dry woodland and arid biota

Identifying genetic markers for a range of phylogenetic utility–From species to family level

Resolving the phylogenetic relationships of closely related species using a small set of loci is challenging as sufficient information may not be captured from a limited sample of the genome. Relying on few loci can also be problematic when conflict between gene-trees arises from incomplete lineage sorting and/or ongoing hybridization, problems especially likely in recently diverged lineages. Here, we developed a method using limited genomic resources that allows identification of many low copy candidate loci from across the nuclear and chloroplast genomes, design probes for target capture and sequence the captured loci. To validate our method we present data from Eucalyptus and Melaleuca, two large and phylogenetically problematic genera within the Myrtaceae family. With one annotated genome, one transcriptome and two whole-genome shotgun sequences of one Eucalyptus and four Melaleuca species, respectively, we identified 212 loci representing 263 kbp for targeted sequence capture and sequencing. Of these, 209 were successfully tested from 47 samples across five related genera of Myrtaceae. The average percentage of reads mapped back to the reference was 57.6% with coverage of more than 20 reads per position across 83.5% of the data. The methods developed here should be applicable across a large range of taxa across all kingdoms. The core methods are very flexible, providing a platform for various genomic resource availabilities and are useful from shallow to deep phylogenies

Identifying genetic markers for a range of phylogenetic utility–From species to family level

Resolving the phylogenetic relationships of closely related species using a small set of loci is challenging as sufficient information may not be captured from a limited sample of the genome. Relying on few loci can also be problematic when conflict between gene-trees arises from incomplete lineage sorting and/or ongoing hybridization, problems especially likely in recently diverged lineages. Here, we developed a method using limited genomic resources that allows identification of many low copy candidate loci from across the nuclear and chloroplast genomes, design probes for target capture and sequence the captured loci. To validate our method we present data from Eucalyptus and Melaleuca, two large and phylogenetically problematic genera within the Myrtaceae family. With one annotated genome, one transcriptome and two whole-genome shotgun sequences of one Eucalyptus and four Melaleuca species, respectively, we identified 212 loci representing 263 kbp for targeted sequence capture and sequencing. Of these, 209 were successfully tested from 47 samples across five related genera of Myrtaceae. The average percentage of reads mapped back to the reference was 57.6% with coverage of more than 20 reads per position across 83.5% of the data. The methods developed here should be applicable across a large range of taxa across all kingdoms. The core methods are very flexible, providing a platform for various genomic resource availabilities and are useful from shallow to deep phylogenies

Perianth evolution and implications for generic delimitation in the eucalypts (Myrtaceae), including the description of the new genus, Blakella

Eucalypts (Myrtaceae tribe Eucalypteae) are currently placed in seven genera. Traditionally, Eucalyptus was defined by its operculum, but when phylogenies placed Angophora, with free sepals and petals, as sister to the operculate bloodwood eucalypts, the latter were segregated into a new genus, Corymbia. Yet, generic delimitation in the tribe Eucalypteae remains uncertain. Here, we address these problems using phylogenetic analysis with the largest molecular data set to date. We captured 101 low-copy nuclear exons from 392 samples representing 266 species. Our phylogenetic analysis used maximum likelihood (IQtree) and multispecies coalescent (Astral). At two nodes critical to generic delimitation, we tested alternative relationships among Arillastrum, Angophora, Eucalyptus, and Corymbia using Shimodaira\u27s approximately unbiased test. Phylogenetic mapping was used to explore the evolution of perianth traits. Monophyly of Corymbia relative to Angophora was decisively rejected. All alternative relationships among the seven currently recognized Eucalypteae genera imply homoplasy in the evolutionary origins of the operculum. Inferred evolutionary transitions in perianth traits are congruent with divergences between major clades, except that the expression of separate sepals and petals in Angophora, which is nested within the operculate genus Corymbia, appears to be a reversal to the plesiomorphic perianth structure. Here, we formally raise Corymbia subg. Blakella to genus rank and make the relevant new combinations. We also define and name three sections within Blakella (Blakella sect. Blakella, Blakella sect. Naviculares, and Blakella sect. Maculatae), and two series within Blakella sect. Maculatae (Blakella ser. Maculatae and Blakella ser. Torellianae). Corymbia is reduced to the red bloodwoods

CCNE1 and survival of patients with tubo-ovarian high-grade serous carcinoma: An Ovarian Tumor Tissue Analysis consortium study

BACKGROUND: Cyclin E1 (CCNE1) is a potential predictive marker and therapeutic target in tubo-ovarian high-grade serous carcinoma (HGSC). Smaller studies have revealed unfavorable associations for CCNE1 amplification and CCNE1 overexpression with survival, but to date no large-scale, histotype-specific validation has been performed. The hypothesis was that high-level amplification of CCNE1 and CCNE1 overexpression, as well as a combination of the two, are linked to shorter overall survival in HGSC. METHODS: Within the Ovarian Tumor Tissue Analysis consortium, amplification status and protein level in 3029 HGSC cases and mRNA expression in 2419 samples were investigated. RESULTS: High-level amplification (>8 copies by chromogenic in situ hybridization) was found in 8.6% of HGSC and overexpression (>60% with at least 5% demonstrating strong intensity by immunohistochemistry) was found in 22.4%. CCNE1 high-level amplification and overexpression both were linked to shorter overall survival in multivariate survival analysis adjusted for age and stage, with hazard stratification by study (hazard ratio [HR], 1.26; 95% CI, 1.08-1.47, p = .034, and HR, 1.18; 95% CI, 1.05-1.32, p = .015, respectively). This was also true for cases with combined high-level amplification/overexpression (HR, 1.26; 95% CI, 1.09-1.47, p = .033). CCNE1 mRNA expression was not associated with overall survival (HR, 1.00 per 1-SD increase; 95% CI, 0.94-1.06; p = .58). CCNE1 high-level amplification is mutually exclusive with the presence of germline BRCA1/2 pathogenic variants and shows an inverse association to RB1 loss. CONCLUSION: This study provides large-scale validation that CCNE1 high-level amplification is associated with shorter survival, supporting its utility as a prognostic biomarker in HGSC

Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

Funder: NCI U24CA211006Abstract: The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that ~80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAF < 15%) and clonal heterogeneity contribute up to 68% of private WGS mutations and 71% of private WES mutations. We observe that ~30% of private WGS mutations trace to mutations identified by a single variant caller in WES consensus efforts. WGS captures both ~50% more variation in exonic regions and un-observed mutations in loci with variable GC-content. Together, our analysis highlights technological divergences between two reproducible somatic variant detection efforts

Genetic analysis of the australian whipbirds and wedgebills illuminates the evolution of their plumage and vocal diversity

Morphological and vocal diversity among closely related species reflects a combination of shared ancestry and recent species-specific adaptations. A small group of Australo-Papuan passerines in the core Corvoidea, the whipbirds and wedgebills (Psophodes, Androphobus), provide an opportunity to explore this. Vocally, the Western Whipbird (Psophodes nigrogularis sensu lato) is very similar to the two species of wedgebills, whereas the sibilant whipcrack-like song of male Eastern Whipbirds is distinctive among the group. Using phylogenetic analysis of mitochondrial DNA we show that Australian whipbirds are not sister taxa but that the Eastern Whipbird is sister to the wedgebills and that the Western Whipbird is sister to the other three members of the group. Wedgebills are nested within the whipbird clade, supporting their current inclusion in Psophodes. The topology and reconstruction of ancestral states suggests the similarity in vocalisation among wedgebills and the Western Whipbird is a result of shared ancestral character states, whereas the whipcrack-like song of the Eastern Whipbirds is autapomorphic.Journal compilatio

Evolutionary consequences of shifts to bird-pollination in the Australian pea-flowered legumes (Mirbelieae and Bossiaeeae)

Background: Interactions with pollinators are proposed to be one of the major drivers of diversity in angiosperms. Specialised interactions with pollinators can lead to specialised floral traits, which collectively are known as a pollination syndrome. While it is thought that specialisation to a pollinator can lead to either an increase in diversity or in some cases a dead end, it is not well understood how transitions among specialised pollinators contribute to changes in diversity. Here, we use evolutionary trait reconstruction of bee-pollination and bird-pollination syndromes in Australian egg-and-bacon peas (Mirbelieae and Bossiaeeae) to test whether transitions between pollination syndromes is correlated with changes in species diversity. We also test for directionality in transitions that might be caused by selection by pollinators or by an evolutionary ratchet in which reversals to the original pollination syndrome are not possible