Aim
Apomixis is a widespread trait in extreme environments worldwide, yet phylogeographical studies for species exhibiting these complex reproductive systems are still limited to temperate zones in ...the Northern Hemisphere. Through analyses of a combination of adult plants and seedlings, and nuclear and chloroplast DNA, we assessed the contemporary genetic outcomes of apomixis and phylogeographical patterns in an arid unglaciated landscape to understand the evolutionary trajectory of apomictic species.
Location
Pilbara bioregion, north‐western Australia.
Taxon
Senna glutinosa subsp. glutinosa.
Materials and Methods
Spatial patterns of genetic diversity and differentiation in three chloroplast regions and 17 nuclear microsatellite markers were evaluated in 480 plants from 20 populations of S. glutinosa subsp. glutinosa across the Pilbara bioregion. We also germinated and genotyped seed for a progeny analysis to quantify polyembryony and the relative frequency of asexual versus sexual reproduction.
Results
We found frequent polyembryony and a high proportion of asexual offspring (84.56%), resulting in low within‐population genotypic diversity. The nuclear dataset identified 72 multilocus lineages (MLLs) with moderate pairwise population genetic fixation and low differentiation among populations with no geographically structured genetic clustering. Chloroplast DNA showed high haplotype diversity and a widespread distribution of haplotypes. Only one peripheral population presented a single unique haplotype and MLL.
Main Conclusions
Analysis of this woody perennial in an arid landscape shows the influence of apomixis on genetic patterns and species persistence. Haplotype diversity was indicative of long‐term persistence within the ancient Pilbara region. Widespread distribution of haplotypes and sharing of several nuclear MLLs among distant populations indicated extensive seed dispersal throughout the study area. The combination of polyploidy, facultative apomixis and extensive seed dispersal maintains genetic variability within local populations and promotes the spread of advantageous genotypes across wide geographical distances. Therefore, apomixis, rather than an evolutionary ‘dead‐end’, can be regarded as a mechanism facilitating evolutionary success of apomictic species in extreme and complex environments.
Understanding how genetic diversity is distributed and maintained within species is a central tenet of evolutionary and conservation biology, yet is understudied in arid regions of the globe. In ...temperate, glaciated environments, high genetic diversity in plant species is frequently found in refugial areas, which are often associated with southern non-glaciated landscapes. In arid, unglaciated environments, landscape features providing mesic conditions are likely to be refugia, although our understanding needs more refinement in these biomes. We test whether refugia and nuclear diversity hotspots occur in high-elevation, topographically complex areas for co-distributed shrubs (Petalostylis labicheoides and Indigofera monophylla; Fabaceae) in the ancient, arid Pilbara bioregion of north-western Australia.
We conducted extensive sampling of the Pilbara (>1400 individuals from 62 widespread populations) to detect patterns in nuclear diversity and structure based on 13-16 microsatellite loci. Evidence of historical refugia was investigated based on patterns of diversity in three non-coding chloroplast (cp) sequence regions for approx. 240 individuals per species. Haplotype relationships were defined with median-joining networks and maximum likelihood phylogenetic trees.
We found cpDNA evidence for a high-elevation refugium in P. labicheoides but not for I. monophylla that instead exhibited extraordinary haplotype diversity and evidence for persistence across a widespread area. Nuclear diversity hotspots occurred in, but were not exclusive to, high-elevation locations and extended to adjacent, low-elevation riparian areas in both species.
Phylogeographic refugia in arid environments may occur in high-elevation areas for some species but not all, and may be influenced by species-specific traits: a mesic montane refugium in P. labicheoides could be related to its preference for growth in water-gaining areas, while a lack of such evidence in I. monophylla could be related to maintenance of cpDNA diversity in a large soil seed bank and dynamic evolutionary history. Mesic environments created by the intersection of topographically complex landscapes with riparian zones can be contemporary reservoirs of genetic diversity in arid landscapes.
Aim: Topographically complex areas are hypothesized to be mesic refugia in arid environments during periods of climatic change. We tested the hypothesis that an elevated and topographically complex ...range has been a historical refugium in an arid environment during Pleistocene climatic oscillations for a widespread eucalypt. Location: Pilbara region, north-west Australia. Methods: We evaluated genetic diversity and differentiation in chloroplast and nuclear genomes using microsatellite loci in 20 populations of Eucalyptus leucophloia from across the distribution in the Pilbara bioregion, including two ranges with differing topographical complexity and elevation. We evaluated phylogeographical structure using Permut and Network analysis, and assessed genetic structure using principle coordinate (PCoA) and Bayesian analyses. Results: We found moderate levels of genetic diversity and low genetic differentiation among populations, typical of widespread eucalypts. There was no evidence of genetic structure across the sampled range. Populations in both the Hamersley and Chichester ranges showed higher levels of chloroplast haplotype and nuclear diversity than those in surrounding areas. Diversity was negatively correlated with evapotranspiration, and positively correlated with precipitation. Main conclusions: Genetic signals of high diversity and low differentiation indicated population persistence throughout historical climate change in ranges, with a signal of expansion in surrounding areas. Our analysis was consistent with the hypothesis of the elevated, topographically complex Hamersley Range acting as a refugium, but revealed an unexpected result of the lower elevation, less rugged Chichester Range also being a refugium. Our results suggest refinement to expectations of environmental characteristics that facilitate persistence, where thresholds of mesic environments for refugia may be lower than expected and moisture availability may be an important contributory aspect of elevation and topographical complexity. In contrast to patterns in reptile species, lack of genetic structure associated with geological substrate and geomorphological features indicates dispersal is not impeded by these landscape features for this widespread eucalypt.
Widespread plant species are expected to maintain genetic diversity and gene flow via pollen and seed dispersal. Stature is a key life history trait that affects seed and potentially pollen ...dispersal, with limited stature associated with limited dispersal and greater genetic differentiation. We sampled Hill’s tabletop wattle (Acacia hilliana) and curry wattle (Acacia spondylophylla), two co‐distributed, widespread, Acacia shrubs of low stature, across the arid Pilbara region of north‐western Australia. Using chloroplast sequence and nuclear microsatellite data we evaluated patterns of population genetic and phylogeographic diversity and structure, demographic signals, ratios of pollen to seed dispersal, evidence for historical refugia, and association between elevation and diversity. Results showed strong phylogeographic (chloroplast, GST = 0.831 and 0.898 for A. hilliana and A. spondylophylla, respectively) and contemporary (nuclear, FST = 0.260 and 0.349 for A. hilliana and A. spondylophylla, respectively) genetic structure in both species. This indicates limited genetic connectivity via seed and pollen dispersal associated with Acacia species of small stature compared to taller tree and shrub acacias across the Pilbara bioregion. This effect of stature on genetic structure is superimposed on moderate levels of genetic diversity that were expected based on widespread ranges (haplotype diversity h = 25 and 12; nuclear diversity He = 0.60 and 0.47 for A. hilliana and A. spondylophylla, respectively). Contemporary genetic structure was congruent at the greater landscape scale, especially in terms of strong genetic differentiation among geographically disjunct populations in less elevated areas. Measures of diversity and connectivity were associated with traits of greater geographic population proximity, population density, population size, and greater individual longevity, and some evidence for range expansion in A. hilliana. Results illustrate that low stature is associated with limited dispersal and greater patterns of genetic differentiation for congenerics in a common landscape and highlight the complex influence of taxon‐specific life history and ecological traits to seed and pollen dispersal.
We assessed phylogeographic and population genetic diversity and structure in two Acacia shrubs of low stature with widespread ranges and co‐distributions across the arid Pilbara region of north‐western Australia: Hill’s tabletop wattle (Acacia hilliana) and curry wattle (Acacia spondylophylla). Both species showed strong phylogeographic and contemporary genetic structure indicating reduced genetic connectivity when compared to taller shrub and tree Acacias in the Pilbara but maintained levels of genetic diversity comparable to that of other widespread Acacia
Phylogeographic studies can be used as a tool to understand the evolutionary history of a landscape, including the major drivers of species distributions and diversity. Extensive research has been ...conducted on phylogeographic patterns of species found in northern hemisphere landscapes that were affected by glaciations, yet the body of literature for older, unaffected landscapes is still underrepresented. The Pilbara region of north-western Australia is an ancient and vast landscape that is topographically complex, consisting of plateaus, gorges, valleys, and ranges, and experiences extreme meteorological phenomena including seasonal cyclonic activity. These features are expected to influence patterns of genetic structuring throughout the landscape either by promoting or restricting the movement of pollen and seed. Whilst a growing body of literature exists for the fauna endemic to this region, less is known about the forces shaping the evolution of plant taxa. In this study we investigate the phylogeography of two iconic Pilbara tree species, the Hamersley Bloodwood (
) and Western Gidgee (
), by assessing patterns of variation and structure in several chloroplast DNA regions and nuclear microsatellite loci developed for each species. Gene flow was found to be extensive in both taxa and there was evidence of long-distance seed dispersal across the region (pollen to seed ratios of 6.67 and 2.96 for
and
, respectively), which may result from flooding and strong wind gusts associated with extreme cyclonic activity. Both species possessed high levels of cpDNA genetic diversity in comparison to those from formerly glaciated landscapes (
= 14 haplotypes,
= 37 haplotypes) and showed evidence of deep lineage diversification occurring from the late Miocene, a time of intensifying aridity in this landscape that appears to be a critical driver of evolution in Pilbara taxa. In contrast to another study, we did not find evidence for topographic features acting as refugia for the widely sampled
.
Failing to test multiple or non-standard variables in studies that investigate the effects of habitat fragmentation on plant populations may limit the detection of unexpected causative relationships. ...Here, we investigated the impacts of habitat fragmentation on the pollination, reproduction, mating system and progeny performance of Eucalyptus wandoo, a foundation tree that is bird and insect pollinated with a mixed-mating system. We explored a range of possible causative mechanisms, including soil properties that are likely to be altered in the agricultural matrix of a landscape that has naturally nutrient-poor soils and secondary soil salinization caused by the removal of native vegetation. We found very strong negative relationships between soil salinity and fruit production, thus providing some of the first evidence for the effects of salinity on reproduction in remnant plant populations. Additionally, we found unexpectedly higher rates of seedling survival in linear populations, most likely driven by increased soil P content from adjacent cereal cropping. Higher rates of seed germination in small populations were related to both higher pollen immigration and greater nutrient availability. Trees in small populations had unexpectedly much higher levels of pollination than in large populations, but they produced fewer seeds per fruit and outcrossing rates did not vary consistently with fragmentation. These results are consistent with small populations having much higher insect abundances but also increased rates of self-pollination, combined with seed abortion mechanisms that are common in the Myrtaceae. This study highlights the need to better understand and mitigate sub-lethal effects of secondary soil salinity in plants growing in agricultural remnants, and indicates that soil properties may play an important role in influencing seed quality.
Aim
Understanding the spatial distribution of genetic variation across a species’ range is a central tenet in evolutionary biology and the ability to predict such patterns is valuable to conservation ...management. Genetic diversity and differentiation may be explained by present‐day niche centrality, historical processes, or morphological variation across a species’ range, yet few studies evaluate these factors concurrently. Moreover, there is a particular lack of knowledge of the influence of these factors in ancient, unglaciated landscapes of the Southern Hemisphere. We investigate these concepts for their influence upon spatial patterns of genetic variation in a widespread plant species in a southern biodiversity hotspot.
Location
South‐western Australia.
Taxon
Calothamnus quadrifidus.
Methods
We use genotyping‐by‐sequencing to assess genome‐wide diversity and differentiation across the range of Calothamnus quadrifidus, a morphologically variable species that occurs over a wide geographic range in an ancient, unglaciated landscape. We correlated the patterns of genetic diversity and differentiation with those predicted under four hypotheses regarding effects of geographic centrality, climatic centrality, historical phylogeography and morphological subspecies.
Results
We found spatial variation in genetic diversity and strong population structuring, and while each hypothesis was consistent with some of these patterns, no hypothesis predicted the full extent of genetic diversity or structure in C. quadrifidus.
Main conclusions
Our results are indicative of a complex evolutionary history, with multiple factors shaping contemporary genetic variation in C. quadrifidus over time, rather than any one major driving factor. This is enabled by the greater capacity to build complex evolutionary signals in ancient, more stable landscapes like the southwest of Western Australia that are not as predictable as those within the younger, post‐glacial landscapes of the Northern Hemisphere. Finally, our study demonstrates the importance of using an interdisciplinary approach to understanding the spatial patterns of genetic variation across species’ ranges and the influence of ecological, geographical and historical factors.
The degree of clonality, interspecific hybridisation and inbreeding in rare species will have significant implications for maintenance of genetic diversity and resilience to environmental change, ...with related implications for immediate conservation management. Using microsatellites, we detected extensive clonality within the rare mallee, Eucalyptus absita, from a highly disturbed agricultural habitat in southwestern Australia. A total of just 16 unique genets, plus five putative hybrids with E. loxophleba, were detected across the known species range and these genets were estimated to be of considerable age. Each location possessed a unique genotype and overall diversity was moderate (H E = 0.547). The outcrossing rate in seedling progeny was low (t ₘ = 0.281), reflecting a rarity of intraspecific sires and minimal inbreeding depression prior to seed dispersal. Of all seedling progeny, up to 19 % were putative hybrids. Our findings indicate that despite rarity and clonality, moderate levels of genetic diversity and the capacity to produce outcrossed seeds is maintained. However, the ongoing maintenance of E. absita genetic diversity is significantly compromised by a high rate of selfing and potential hybridisation in seedling progeny. Seeds collected for long-term storage or rehabilitation should be screened for inbreeding and hybridisation rates to improve conservation outcomes. All existing adults represent a unique portion of the genepool for conservation.
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