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17 pages, 4900 KiB

Open AccessArticle

Allele Surfing and Holocene Expansion of an Australian Fig (Ficus—Moraceae)

by Brendan C. Wilde, Susan Rutherford, Jia-Yee S. Yap and Maurizio Rossetto

Diversity 2021, 13(6), 250; https://doi.org/10.3390/d13060250 - 07 Jun 2021

Cited by 1 | Viewed by 3392

The creek sandpaper fig of southeastern Australia, Ficus coronata Spin, is culturally significant to Australian traditional owners who made use of the leaves to smooth timber and ate the fruit. The species is thought to have a long history on the continent, with [...] Read more.

The creek sandpaper fig of southeastern Australia, Ficus coronata Spin, is culturally significant to Australian traditional owners who made use of the leaves to smooth timber and ate the fruit. The species is thought to have a long history on the continent, with some suggesting a Gondwanan origin. However, distributional patterns and overall ecology suggest a recent expansion across suitable habitats. We used landscape genomic techniques and environmental niche modelling to reconstruct its history and explore whether the species underwent a recent and rapid expansion along the east coast of New South Wales. Genomic analysis of 178 specimens collected from 32 populations throughout the species’ New South Wales distribution revealed a lack of genetic diversity and population structure. Some populations at the species’ southern and western range limits displayed unexpected diversity, which appears to be the result of allele surfing. Field work and genetic evidence suggest a Holocene expansion which may have increased since European colonisation. We also present a novel method for detecting allele surfing—MAHF (minor allele at highest frequency). Full article

(This article belongs to the Special Issue Evolutionary Ecology and Conservation of Native Plants)

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24 pages, 26133 KiB

Open AccessArticle

Genetic Distinctiveness but Low Diversity Characterizes Rear-Edge Thuja standishii (Gordon) Carr. (Cupressaceae) Populations in Southwest Japan

by James R. P. Worth, Ichiro Tamaki, Ikutaro Tsuyama, Peter A. Harrison, Kyoko Sugai, Hitoshi Sakio, Mineaki Aizawa and Satoshi Kikuchi

Diversity 2021, 13(5), 185; https://doi.org/10.3390/d13050185 - 28 Apr 2021

Cited by 3 | Viewed by 2512

Abstract

Rear-edge populations are of significant scientific interest because they can contain allelic variation not found in core-range populations. However, such populations can differ in their level of genetic diversity and divergence reflecting variation in life-history traits, demographic histories and human impacts. Using 13 [...] Read more.

Rear-edge populations are of significant scientific interest because they can contain allelic variation not found in core-range populations. However, such populations can differ in their level of genetic diversity and divergence reflecting variation in life-history traits, demographic histories and human impacts. Using 13 EST-microsatellites, we investigated the genetic diversity and differentiation of rear-edge populations of the Japanese endemic conifer Thuja standishii (Gordon) Carr. in southwest Japan from the core-range in northeast Japan. Range-wide genetic differentiation was moderate (Fst = 0.087), with northeast populations weakly differentiated (Fst = 0.047), but harboring high genetic diversity (average population-level Ar = 4.76 and Ho = 0.59). In contrast, rear-edge populations were genetically diverged (Fst = 0.168), but contained few unique alleles with lower genetic diversity (Ar = 3.73, Ho = 0.49). The divergence between rear-edge populations exceeding levels observed in the core-range and results from ABC analysis and species distribution modelling suggest that these populations are most likely relicts of the Last Glacial Maximum. However, despite long term persistence, low effective population size, low migration between populations and genetic drift have worked to promote the genetic differentiation of southwest Japan populations of T. standishii without the accumulation of unique alleles. Full article

(This article belongs to the Special Issue Evolutionary Ecology and Conservation of Native Plants)

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17 pages, 2817 KiB

Open AccessArticle

All Populations Matter: Conservation Genomics of Australia’s Iconic Purple Wattle, Acacia purpureopetala

by Marlien M. van der Merwe, Jia-Yee S. Yap, Peter D. Wilson, Helen T. Murphy and Andrew Ford

Diversity 2021, 13(4), 139; https://doi.org/10.3390/d13040139 - 25 Mar 2021

Cited by 7 | Viewed by 2130

Abstract

Maximising genetic diversity in conservation efforts can help to increase the chances of survival of a species amidst the turbulence of the anthropogenic age. Here, we define the distribution and extent of genomic diversity across the range of the iconic but threatened Acacia [...] Read more.

Maximising genetic diversity in conservation efforts can help to increase the chances of survival of a species amidst the turbulence of the anthropogenic age. Here, we define the distribution and extent of genomic diversity across the range of the iconic but threatened Acacia purpureopetala, a beautiful sprawling shrub with mauve flowers, restricted to a few disjunct populations in far north Queensland, Australia. Seed production is poor and germination sporadic, but the species occurs in abundance at some field sites. While several thousands of SNP markers were recovered, comparable to other Acacia species, very low levels of heterozygosity and allelic variation suggested inbreeding. Limited dispersal most likely contributed towards the high levels of divergence amongst field sites and, using a generalised dissimilarity modelling framework amongst environmental, spatial and floristic data, spatial distance was found to be the strongest factor explaining the current distribution of genetic diversity. We illustrate how population genomic data can be utilised to design a collecting strategy for a germplasm conservation collection that optimises genetic diversity. For this species, inclusion of all field sites will capture maximum genetic diversity for both in situ and ex situ conservation. Assisted cross pollination, within and between field sites and genetically structured groups, is recommended to enhance heterozygosity particularly at the most disjunct sites and further fragmentation should be discouraged to avoid loss of genetic connectivity. Full article

(This article belongs to the Special Issue Evolutionary Ecology and Conservation of Native Plants)

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16 pages, 5033 KiB

Open AccessArticle

Managing Genetic Diversity and Representation in Banksia marginata (Proteaceae) Seed Production Areas Used for Conservation and Restoration

by Linda Broadhurst, David Bush and Jim Begley

Diversity 2021, 13(2), 39; https://doi.org/10.3390/d13020039 - 21 Jan 2021

Cited by 1 | Viewed by 2328

Abstract

Landscape degradation is a major threat to global biodiversity that is being further exacerbated by climate change. Halting or reversing biodiversity decline using seed-based restoration requires tons of seed, most of which is sourced from wild populations. However, in regions where restoration is [...] Read more.

Landscape degradation is a major threat to global biodiversity that is being further exacerbated by climate change. Halting or reversing biodiversity decline using seed-based restoration requires tons of seed, most of which is sourced from wild populations. However, in regions where restoration is most urgent, wild seed sources are often fragmented, declining and producing seed with low genetic diversity. Seed production areas (SPAs) can help to reduce the burden of collecting native seed from remnant vegetation, improve genetic diversity in managed seed crops and contribute to species conservation. Banksia marginata (Proteaceae) is a key restoration species in south-eastern Australia but is highly fragmented and declining across much of its range. We evaluated genetic diversity, population genetic structure and relatedness in two B. marginata SPAs and the wild populations from which the SPA germplasm was sourced. We found high levels of relatedness within most remnants and that the population genetic structure was best described by three groups of trees. We suggest that SPAs are likely to be important to meet future native seed demand but that best practice protocols are required to assist land managers design and manage these resources including genetic analyses to guide the selection of germplasm. Full article

(This article belongs to the Special Issue Evolutionary Ecology and Conservation of Native Plants)

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20 pages, 1498 KiB

Open AccessArticle

Recently Naturalized Paraserianthes lophantha subsp. lophantha Displays Contrasting Genetic Diversity and Climate Relationships Compared to Native Populations

by Gillian K. Brown, Elizabeth A. James, Catherine L. Simmons and Collin W. Ahrens

Diversity 2020, 12(11), 422; https://doi.org/10.3390/d12110422 - 10 Nov 2020

Cited by 3 | Viewed by 2597

Abstract

Paraseriantheslophantha subsp. lophantha (Leguminosae) is native to southwestern Australia, but has become naturalized in eastern Australia and in countries around the world. Previous studies have investigated the introduction sources for P. lophantha subsp. lophantha overseas, but here, we expand on the knowledge [...] Read more.

Paraseriantheslophantha subsp. lophantha (Leguminosae) is native to southwestern Australia, but has become naturalized in eastern Australia and in countries around the world. Previous studies have investigated the introduction sources for P. lophantha subsp. lophantha overseas, but here, we expand on the knowledge of genetic patterns in its native and naturalized range in Australia. Genetic patterns were examined using nine nuclear microsatellite loci and three chloroplast DNA markers. The native populations exhibited phylogeographic patterns, including north-south differentiation, and a genetic signal related to temperature gradients. Naturalized Australian populations displayed lower overall genetic variation and no phylogeographic patterns. Several naturalized populations separated by large distances (350–650 km) shared multi-locus genotypes, supporting the notion of a shared source of germplasm and possible inbreeding due to human-mediated introductions from a limited number of individuals and/or source populations within the native range. We advocate that management strategies are tailored to the distinct conservation aims underpinning conservation in native or naturalized populations. Within the native distribution, management should have a long-term aim to replicate historical evolutionary processes, whereas in naturalized populations, immediate actions may be required to reduce the abundance of P. lophantha subsp. lophantha and minimize its invasive impact on the recipient vegetation. Full article

(This article belongs to the Special Issue Evolutionary Ecology and Conservation of Native Plants)

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12 pages, 3180 KiB

Open AccessArticle

Genomic Phylogeography of Gymnocarpos przewalskii (Caryophyllaceae): Insights into Habitat Fragmentation in Arid Northwestern China

by Hong-Xiang Zhang, Qian Wang and Su-Wen Jia

Diversity 2020, 12(9), 335; https://doi.org/10.3390/d12090335 - 31 Aug 2020

Cited by 14 | Viewed by 3005

Abstract

Extensive range of deserts and gobis (rocks) had promoted habitat fragmentation of species in arid northwestern China. Distribution of endangered Gymnocarpos przewalskii Maxim. covers most of gobis (rocks) and desert terrain across arid regions of northwestern China. In the present study, we had [...] Read more.

Extensive range of deserts and gobis (rocks) had promoted habitat fragmentation of species in arid northwestern China. Distribution of endangered Gymnocarpos przewalskii Maxim. covers most of gobis (rocks) and desert terrain across arid regions of northwestern China. In the present study, we had employed genomic phylogeographical analysis to investigate population structure of G. przewalskii and test the effect of environmental conditions on spatial pattern of genetic diversity. Results showed four groups were identified from east to west: Edge of the Alxa Desert, Hexi Corridor, Hami Basin, and North edge of the Tarim Basin. Genetic diversity was at an equal level among four groups. General linear model (GLM) analysis showed spatial pattern of genetic diversity was significant correlated with three habitat variables including habitat suitability at present (N_pre) and last glacial maximum (LGM) (N_LGM) periods, and locality habitat stability (N_Stab). It concluded that habitat fragmentation had triggered lineage divergences of G. przewalskii in response to long-term aridification. Genome-wide single nucleotide polymorphisms (SNPs) could increase the ability of clarifying population structures in comparison with traditional molecular markers. Spatial pattern of genetic diversity was determined by fragmented habitats with high habitat suitability (N_pre and N_LGM) and stability (N_Stab). At last, we propose to establish four conservation units which are in consistent with the population grouping to maintain the genetic integrity of this endangered species. Full article

(This article belongs to the Special Issue Evolutionary Ecology and Conservation of Native Plants)

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17 pages, 2272 KiB

Open AccessFeature PaperArticle

Perceptions of Similarity Can Mislead Provenancing Strategies—An Example from Five Co-Distributed Acacia Species

by Maurizio Rossetto, Peter D. Wilson, Jason Bragg, Joel Cohen, Monica Fahey, Jia-Yee Samantha Yap and Marlien van der Merwe

Diversity 2020, 12(8), 306; https://doi.org/10.3390/d12080306 - 06 Aug 2020

Cited by 7 | Viewed by 2921

Abstract

Ecological restoration requires balancing levels of genetic diversity to achieve present-day establishment as well as long-term sustainability. Assumptions based on distributional, taxonomic or functional generalizations are often made when deciding how to source plant material for restoration. We investigate this assumption and ask [...] Read more.

Ecological restoration requires balancing levels of genetic diversity to achieve present-day establishment as well as long-term sustainability. Assumptions based on distributional, taxonomic or functional generalizations are often made when deciding how to source plant material for restoration. We investigate this assumption and ask whether species-specific data is required to optimize provenancing strategies. We use population genetic and environmental data from five congeneric and largely co-distributed species of Acacia to specifically ask how different species-specific genetic provenancing strategies are based on empirical data and how well a simple, standardized collection strategy would work when applied to the same species. We find substantial variability in terms of patterns of genetic diversity and differentiation across the landscape among these five co-distributed Acacia species. This variation translates into substantial differences in genetic provenancing recommendations among species (ranging from 100% to less than 1% of observed genetic variation across species) that could not have been accurately predicted a priori based on simple observation or overall distributional patterns. Furthermore, when a common provenancing strategy was applied to each species, the recommended collection areas and the evolutionary representativeness of such artificially standardized areas were substantially different (smaller) from those identified based on environmental and genetic data. We recommend the implementation of the increasingly accessible array of evolutionary-based methodologies and information to optimize restoration efforts. Full article

(This article belongs to the Special Issue Evolutionary Ecology and Conservation of Native Plants)

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18 pages, 5976 KiB

Open AccessArticle

Increased Genetic Diversity via Gene Flow Provides Hope for Acacia whibleyana, an Endangered Wattle Facing Extinction

by Colette Blyth, Matthew J. Christmas, Doug C. Bickerton, Renate Faast, Jasmin G. Packer, Andrew J. Lowe and Martin F. Breed

Diversity 2020, 12(8), 299; https://doi.org/10.3390/d12080299 - 30 Jul 2020

Cited by 12 | Viewed by 5822

Abstract

In this paper we apply a conservation genomics approach to make evidence-based management recommendations for Acacia whibleyana, an endangered shrub endemic to Eyre Peninsula, South Australia. We used population genomic analysis to assess genetic connectivity, diversity, and historical inbreeding across all known stands [...] Read more.

In this paper we apply a conservation genomics approach to make evidence-based management recommendations for Acacia whibleyana, an endangered shrub endemic to Eyre Peninsula, South Australia. We used population genomic analysis to assess genetic connectivity, diversity, and historical inbreeding across all known stands of the species sampling remnant stands, revegetated stands of unknown origin, and a post-fire seedling cohort. Our results indicate a degree of historical connectivity across the landscape, but habitat loss and/or pollinator community disruption are potential causes of strong genetic structure across the remnant stands. Remnant stands had low genetic diversity and showed evidence of historical inbreeding, but only low levels of intra-stand relatedness indicating that risks of contemporary inbreeding are low. Analysis of a post-fire first generation cohort of seedlings showed they likely resulted from intra-stand matings, resulting in reduced genetic diversity compared to the parents. However, admixed seedlings in this cohort showed an increase in heterozygosity relative to likely sources and the non-admixed seedlings of the same stand. Assisted inter-stand gene flow may prove an effective management strategy to boost heterozygosity and corresponding increases in adapting capacity in this endangered species. Full article

(This article belongs to the Special Issue Evolutionary Ecology and Conservation of Native Plants)

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Review

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10 pages, 254 KiB

Open AccessReview

Conserving Refugia: What Are We Protecting and Why?

by Maurizio Rossetto and Robert Kooyman

Diversity 2021, 13(2), 67; https://doi.org/10.3390/d13020067 - 07 Feb 2021

Cited by 9 | Viewed by 3362

Abstract

Refugia play an important role in contributing to the conservation of species and communities by buffering environmental conditions over time. As large natural landscapes worldwide are declining and are increasingly threatened by extreme events, critical decision-making in biological conservation depends on improved understanding [...] Read more.

Refugia play an important role in contributing to the conservation of species and communities by buffering environmental conditions over time. As large natural landscapes worldwide are declining and are increasingly threatened by extreme events, critical decision-making in biological conservation depends on improved understanding of what is being protected by refugia and why. We provide three novel definitions for refugia (i.e., persistent, future, and temporary) that incorporate ecological and evolutionary dynamics into a land management decision framework and are applicable across changing temporal and spatial settings. Definitions are supported by identification, core value, and management strategy criteria to assist short- and long-term decision-making. We illustrate these concepts using the World Heritage Gondwana Rainforests (WHGR) of eastern Australia, briefly exploring the spatial and temporal factors that can inform the development of conservation management strategies following the extreme fire events of 2019–2020. For the WHGR, available knowledge can be used to protect critical assets by recognizing and implementing buffer zones and corridor connections, and by undertaking emergency translocations of target species into safe areas that will act as future refugia. More broadly, we suggest that the identification and protection of ecological and evolutionary processes across varying temporal and spatial scales is central to securing improved biodiversity conservation outcomes. Full article

(This article belongs to the Special Issue Evolutionary Ecology and Conservation of Native Plants)

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