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

Nine accessions of Bambara groundnut (Vigna subterranea (L.) Verdc.,syn. Voandzeia subterranea (L.) Thouars ex DC.) obtained from National Centre for Genetic Resources and Biotechnology (NACGRAB), Ibadan, Oyo state, were assessed for their genetic and phylogenetic relatedness through electrophoretic analysis of the seed proteins. 0.2g of the seeds were weighed and macerated with mortar and pestle in 0.2M phosphate buffer containing 0.133M of acid (NaH2PO4) and 0.067 of base (Na2HPO4) at pH 6.5. Protein characterization with standard marker revealed that the seeds of the nine accessions contained proteins (B.S.A, Oval Albumin, Pepsinogen, Trypsinogen and Lysozyme) with molecular weights ranging from 66kda and above, 45 – 65 kDa, 44 – 33 kda, 32-24 kDa and 23-14 kDa, respectively. The student T-test revealed that accessions B, C, E, F, H and I have molecular weights not significantly different from one another (P<0.05) while samples A, D and G showed significantly different values (P>0.05). All the accessions had at least two proteins and two major bands in common. The study revealed intra-specific similarities and genetic diversity in protein contents among the nine accessions of Bambara groundnut (Vigna subterraranea (L.) Verdc.syn

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Genetic diversity and phylogenetic behavior of some minor legumes

International Journal of Plant Biology ◽

10.4081/pb.2016.6136 ◽

2016 ◽

Vol 7 (1) ◽

Author(s):

James Oludare Agbolade ◽

Ronke Justina Komolafe

Keyword(s):

Genetic Diversity ◽

Principal Component ◽

Calyx Lobe ◽

Descriptive Statistics ◽

International Institute ◽

Mean Values ◽

Phylogenetic Relatedness ◽

Petal Length ◽

Morphological Differences ◽

Range Test

Twenty-four accessions of twelve species minor legumes collected from the germplasm unit of the International Institute of Tropical Agriculture Ibadan, Nigeria were evaluated for their genetic diversities and phylogenetic relatedness. The accessions were planted into plots of 5 ridges of 5 meters long, spaced 1 meter apart and replicated three times at the Federal University Oye-Ekiti Teaching and Research Farm. The diversity and the relative phylogeny of the accessions were assessed through their floral morphological differences and the mean values between two accessions were evaluated by descriptive statistics. Principal component analysis was employed to identify the most discriminatory floral morphological traits and the similarities among the 24 accessions were assessed by cluster analysis (CA). Descriptive statistics through Duncan multiple range test adopted revealed genetic diversity and phylogenetic relatedness among the accessions. The first two principal component axes explained 64.66% of the total floral morphological variation. Standard petal length, calyx lobe length and stipule length contributed most of the variations in the legume accession. CA grouped the 24 accessions into six clusters. The study revealed intra-specific similarities and inter-specific floral morphological differences among the studied accessions.

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Genome-Scale Phylogeny and Evolutionary Analysis of Ross River Virus Reveals Periodic Sweeps of Lineage Dominance in Western Australia, 1977–2014

Journal of Virology ◽

10.1128/jvi.01234-19 ◽

2019 ◽

Vol 94 (2) ◽

Cited By ~ 2

Author(s):

Alice Michie ◽

Vijaykrishna Dhanasekaran ◽

Michael D. A. Lindsay ◽

Peter J. Neville ◽

Jay Nicholson ◽

...

Keyword(s):

Genetic Diversity ◽

Western Australia ◽

Evolutionary History ◽

Gene Analysis ◽

Ross River Virus ◽

Whole Genome ◽

Evolutionary Analysis ◽

Genotype 4 ◽

E2 Gene ◽

Genome Scale

ABSTRACT Ross River virus (RRV), an alphavirus of the Togaviridae family, is the most medically significant mosquito-borne virus of Australia. Past RRV phylogenetic and evolutionary analyses have been based on partial genome analyses only. Three geographically distinct RRV lineages, the Eastern, the Western, and the supposedly extinct North-Eastern lineage, were classified previously. We sought to expand on past phylogenies through robust genome-scale phylogeny to better understand RRV genetic diversity and evolutionary dynamics. We analyzed 106 RRV complete coding sequences, which included 13 genomes available on NCBI and 94 novel sequences derived for this study, sampled throughout Western Australia (1977–2014) and during the substantial Pacific Islands RRV epidemic (1979–1980). Our final data set comprised isolates sampled over 59 years (1959–2018) from a range of locations. Four distinct genotypes were defined, with the newly described genotype 4 (G4) found to be the contemporary lineage circulating in Western Australia. The prior geographical classification of RRV lineages was not supported by our findings, with evidence of geographical and temporal cocirculation of distinct genetic groups. Bayesian Markov chain Monte Carlo (MCMC) analysis revealed that RRV lineages diverged from a common ancestor approximately 94 years ago, with distinct lineages emerging roughly every 10 years over the past 50 years in periodic bursts of genetic diversity. Our study has enabled a more robust analysis of RRV evolutionary history and resolved greater genetic diversity that had been previously defined by partial E2 gene analysis. IMPORTANCE Ross River virus (RRV) causes the most common mosquito-borne infection in Australia and causes a significant burden of suffering to infected individuals as well as being a large burden to the Australian economy. The genetic diversity of RRV and its evolutionary history have so far only been studied using partial E2 gene analysis with a limited number of isolates. Robust whole-genome analysis has not yet been conducted. This study generated 94 novel near-whole-genome sequences to investigate the evolutionary history of RRV to better understand its genetic diversity through comprehensive whole-genome phylogeny. A better understanding of RRV genetic diversity will enable better diagnostics, surveillance, and potential future vaccine design.

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Groundwater oligochaetes show complex genetic patterns of distribution in the Pilbara region of Western Australia

Invertebrate Systematics ◽

10.1071/is14037 ◽

2015 ◽

Vol 29 (5) ◽

pp. 405 ◽

Cited By ~ 6

Author(s):

Louise Brown ◽

Terrie Finston ◽

Garth Humphreys ◽

Stefan Eberhard ◽

Adrian Pinder

Keyword(s):

Genetic Diversity ◽

Western Australia ◽

Surface Waters ◽

Ecological Niches ◽

Mitochondrial Coi ◽

Groundwater Fauna ◽

Ecological Requirements ◽

Large Size ◽

Geographic Patterns ◽

Genetic Patterns

Patterns of genetic diversity in the groundwater fauna of Australia have largely focused on obligate stygobites of relatively large size, namely, crustaceans. Oligochaete worms, with their smaller size and broader ecological niches, provide a contrasting model in which to examine such patterns. Genetic diversity in subterranean oligochaetes in the Pilbara region of Western Australia were examined using one nuclear (18S) and two mitochondrial (COI, 12S) regions. The observed variation was assessed at three levels of hydrology – river basin, creek catchment, and individual bore or site – to document geographic patterns. Most species appeared to be restricted to an individual catchment; however, five species, representing three families, were widespread, with some haplotypes being shared between bores, catchments and even basins. General patterns suggest that while hydrology plays a role in the distribution of oligochaete species, it does not always confine them to catchments, in contrast to patterns observed in groundwater isopods and amphipods in the region. We suggest that intrinsic characteristics of oligochaetes, such as body size, shape, reproductive strategy and ecological requirements, may have allowed them greater dispersal within the subterranean biome of the Pilbara. In particular, oligochaetes may occupy subterranean and surface waters, increasing their opportunities for dispersal.

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Variation in reproductive effort, genetic diversity and mating systems across Posidonia australis seagrass meadows in Western Australia

AoB Plants ◽

10.1093/aobpla/plaa038 ◽

2020 ◽

Vol 12 (4) ◽

Author(s):

Elizabeth A Sinclair ◽

Jane M Edgeloe ◽

Janet M Anthony ◽

John Statton ◽

Martin F Breed ◽

...

Keyword(s):

Genetic Diversity ◽

Mating System ◽

Western Australia ◽

Reproductive Effort ◽

Genetic Data ◽

Fruit Production ◽

Mixed Mating ◽

Mixed Mating System ◽

Shark Bay ◽

Range Edge

Abstract Populations at the edges of their geographical range tend to have lower genetic diversity, smaller effective population sizes and limited connectivity relative to centre of range populations. Range edge populations are also likely to be better adapted to more extreme conditions for future survival and resilience in warming environments. However, they may also be most at risk of extinction from changing climate. We compare reproductive and genetic data of the temperate seagrass, Posidonia australis on the west coast of Australia. Measures of reproductive effort (flowering and fruit production and seed to ovule ratios) and estimates of genetic diversity and mating patterns (nuclear microsatellite DNA loci) were used to assess sexual reproduction in northern range edge (low latitude, elevated salinities, Shark Bay World Heritage Site) and centre of range (mid-latitude, oceanic salinity, Perth metropolitan waters) meadows in Western Australia. Flower and fruit production were highly variable among meadows and there was no significant relationship between seed to ovule ratio and clonal diversity. However, Shark Bay meadows were two orders of magnitude less fecund than those in Perth metropolitan waters. Shark Bay meadows were characterized by significantly lower levels of genetic diversity and a mixed mating system relative to meadows in Perth metropolitan waters, which had high genetic diversity and a completely outcrossed mating system. The combination of reproductive and genetic data showed overall lower sexual productivity in Shark Bay meadows relative to Perth metropolitan waters. The mixed mating system is likely driven by a combination of local environmental conditions and pollen limitation. These results indicate that seagrass restoration in Shark Bay may benefit from sourcing plant material from multiple reproductive meadows to increase outcrossed pollen availability and seed production for natural recruitment.

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Convergent evolution of caffeine in plants by co-option of exapted ancestral enzymes

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1602575113 ◽

2016 ◽

Vol 113 (38) ◽

pp. 10613-10618 ◽

Cited By ~ 45

Author(s):

Ruiqi Huang ◽

Andrew J. O’Donnell ◽

Jessica J. Barboline ◽

Todd J. Barkman

Keyword(s):

Genetic Diversity ◽

Plant Defense ◽

Plant Species ◽

Convergent Evolution ◽

Flowering Plant ◽

Phylogenetic Relatedness ◽

Future Studies ◽

Biochemical Pathways ◽

Caffeine Synthase ◽

Caffeine Biosynthesis

Convergent evolution is a process that has occurred throughout the tree of life, but the historical genetic and biochemical context promoting the repeated independent origins of a trait is rarely understood. The well-known stimulant caffeine, and its xanthine alkaloid precursors, has evolved multiple times in flowering plant history for various roles in plant defense and pollination. We have shown that convergent caffeine production, surprisingly, has evolved by two previously unknown biochemical pathways in chocolate, citrus, and guaraná plants using either caffeine synthase- or xanthine methyltransferase-like enzymes. However, the pathway and enzyme lineage used by any given plant species is not predictable from phylogenetic relatedness alone. Ancestral sequence resurrection reveals that this convergence was facilitated by co-option of genes maintained over 100 million y for alternative biochemical roles. The ancient enzymes of the Citrus lineage were exapted for reactions currently used for various steps of caffeine biosynthesis and required very few mutations to acquire modern-day enzymatic characteristics, allowing for the evolution of a complete pathway. Future studies aimed at manipulating caffeine content of plants will require the use of different approaches given the metabolic and genetic diversity revealed by this study.

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Wide Variation in Virulence and Genetic Diversity of Binucleate Rhizoctonia Isolates Associated with Root Rot of Strawberry in Western Australia

PLoS ONE ◽

10.1371/journal.pone.0055877 ◽

2013 ◽

Vol 8 (2) ◽

pp. e55877 ◽

Cited By ~ 24

Author(s):

Xiangling Fang ◽

Patrick M. Finnegan ◽

Martin J. Barbetti

Keyword(s):

Genetic Diversity ◽

Western Australia ◽

Root Rot ◽

Binucleate Rhizoctonia

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Genetic viability of a reintroduced population of south-western common brushtail possum (Trichosurus vulpecula hypoleucus), Western Australia

Pacific Conservation Biology ◽

10.1071/pc19031 ◽

2020 ◽

Vol 26 (3) ◽

pp. 282

Author(s):

Lara Semple ◽

Kym Ottewell ◽

Colleen Sims ◽

Henner Simianer ◽

Margaret Byrne

Keyword(s):

Genetic Diversity ◽

Western Australia ◽

Sign Test ◽

Brushtail Possum ◽

Trichosurus Vulpecula ◽

Tissue Samples ◽

Reintroduced Population ◽

Common Brushtail Possum ◽

Source Populations ◽

The Impact

This study focused on a reintroduced population of south-western common brushtail possum (Trichosurus vulpecula hypoleucus) to assess genetic variability and inform future management strategies. Individuals were translocated to Matuwa Kurarra-Kurarra Indigenous Protected Area, Western Australia, from four source populations, but subsequent monitoring has indicated a 50% reduction in population size from original founder numbers in the eight years since establishment. Tissue samples from three of the four source populations and an additional four comparative sites (n=140 animals total) were analysed using 13 microsatellite loci. Inbreeding was lower and heterozygosity was higher in the translocated Matuwa population than in two of the source populations studied, highlighting the benefits of promoting outbreeding through the use of multiple source populations in translocations. However, allelic richness at Matuwa is low relative to two of the source populations, suggesting the impact of population bottlenecks on genetic diversity, which was supported by significant allele frequency mode shift and Wilcoxon rank sign test for heterozygosity excess tests for genetic bottlenecks. Despite the genetic health of the population being stronger than predicted, this population is still at risk due to environmental factors, small size and fragmentation. This is the first study to document patterns of genetic diversity and to highlight issues with translocation for this subspecies and adds to the limited literature illustrating how outbreeding can be used for conservation purposes.

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Divergent lineages in the heath mouse (Pseudomys shortridgei) are indicative of major contraction to geographically isolated refugia on the eastern and western sides of Australia during the early Pleistocene

Australian Journal of Zoology ◽

10.1071/zo08097 ◽

2009 ◽

Vol 57 (1) ◽

pp. 41 ◽

Cited By ~ 9

Author(s):

Maria Salinas ◽

Michael Bunce ◽

Damien Cancilla ◽

Deryn L. Alpers ◽

Peter B. S. Spencer

Keyword(s):

Genetic Diversity ◽

Western Australia ◽

Early Pleistocene ◽

Evolutionary Significant Units ◽

Australian Continent ◽

D Loop ◽

Nuclear Microsatellite ◽

Genetic Clusters ◽

Significant Divergence ◽

Nuclear Loci

The heath mouse (Pseudomys shortridgei) is a locally rare species; it was considered extinct in Western Australia until its rediscovery 20 years ago. It is not often detected in faunal surveys and is confined to two ecologically distinct habitats on either side of the Australian continent. An important and immediate conservation question has been to determine the genetic diversity within each of its current habitats and to determine the differences between the geographically separate populations. Measures of genetic differentiation amongst P. shortridgei populations in their eastern (Victoria) and western (Western Australia) distribution were estimated using nuclear (microsatellite loci) and partial sequence of mitochondrial DNA (427 bp Cytochrome b gene and 637 bp of the D-loop). Both markers identified differences between the east- and west-coast populations. MtDNA data showed significant divergence between populations with monophyly within them, and nuclear loci investigated also showed two clear genetic clusters based on Bayesian inference. As a result of these findings, we suggest that the heath mouse comprises two highly divergent (but genetically diverse) lineages and the aridity of the Nullarbor Plain has clearly been a barrier for dispersal since the early Pleistocene (~1.43 million years ago). The populations either side of the Nullarbor Plain are genetically differentiated and should be defined as separate Evolutionary Significant Units (ESUs).

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Impact of CIMMYT varieties on the genetic diversity of wheat in Australia, 1973-1993

Australian Journal of Agricultural Research ◽

10.1071/a97065 ◽

1998 ◽

Vol 49 (2) ◽

pp. 175 ◽

Cited By ~ 18

Author(s):

John P. Brennan ◽

Paul N. Fox

Keyword(s):

Genetic Diversity ◽

Western Australia ◽

National Level ◽

South Australia ◽

Genetic Base ◽

Wheat Improvement ◽

The Impact

Wheats derived from germplasm developed by the International Maize and Wheat Improvement Center (CIMMYT) have been grown widely in Australia since the early 1970s. The impact of CIMMYT germplasm on the genetic diversity of Australian wheats over the 20 years to 1993 is examined. On average, the diversity at a national level remained relatively high throughout the period, but this finding varied markedly between States. While there was significant increase in diversity in South Australia and Western Australia, there was a narrowing of the genetic base of varieties grown in the eastern States, especially Victoria, accompanying the widespread use of CIMMYT germplasm.

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