Spatial patterns of genetic diversity among Australian alpine flora communities revealed by comparative phylogenomics

Abstract

Aim: The alpine region of mainland Australia is one of the world's 187 biodiversity hotspots. Genetic analyses of Australian alpine fauna indicate high levels of endemism on fine spatial scales, unlike Northern Hemisphere alpine systems where shallow genetic differentiation is typically observed among populations. These discrepancies have been attributed to differences in elevation and influence from glacial activity, and point to a unique phylogeographic history affecting Australian alpine biodiversity. To test generality of these findings across Australian alpine biota, we assessed patterns of genetic structure across plant species.Location: The Australian Alps, Victoria, eastern Australia. Methods:We used an economical pooled genotyping-by-sequencing (GBS) approach to examine patterns of genetic diversity among seven widespread species including shrubs and forbs from 16 mountain summits in the Australian Alpine National Park. Patterns of genetic structure among summit populations for each species were inferred from an average of 2,778 independent SNP loci using Bayesian phylogenomic inference and clustering approaches.Results: SNP results were consistent across species in identifying deep evolutionary splits among summit communities from the Northern and Central Victorian Alpine regions. These patterns of genetic structure are also consistent with those previously reported for invertebrate and mammal taxa. However, local genetic structure was less pronounced in the plants, supporting the notion that population connectivity tends to be higher in plant species.Main conclusion: There is deep lineage diversification between the North and Central Victorian Alpine regions, reflecting a high level of endemism. These findings differ from those reported for alpine biodiversity from New South Wales and much of the Northern Hemisphere, and support the notion that genetic diversity is typically greatest in areas least affected by historical ice sheet formation. We discuss the implications of our findings in the context of conservation planning, and highlight the benefits of this rapid and cost-effective genome scan approach for characterizing evolutionary processes at multispecies and landscape scales. K E Y W O R D S

Global patterns and drivers of alpine plant species richness

“…When accounting for the extent of the local alpine area, the Drakensberg (Afrotropics) and the Australian Alps (Australasia) emerged as centres of alpine plant richness of the Southern Hemisphere. Indeed, the high‐elevation plateau of the Drakensberg has been widely recognized as a continental hotspot of botanical diversity (Brand et al., 2019; Carbutt, 2019), and the Australian Alps have been listed among the main national areas of plant species richness (Bell et al., 2018; Crisp et al, 2001). Other regions showed lower species richness, with no clear distinctions among different realms or latitudes.…”

Temporal changes in genetic diversity and forage yield of perennial ryegrass in monoculture and in combination with red clover in swards

“…The combination of pool-seq and GBS (pool-GBS) is a promising strategy for assessing genetic diversity among populations on a genome-wide scale [ 57 ]. This approach has previously been applied to perennial ryegrass [ 26 , 27 ], barley [ 58 , 59 ], multiple species of alpine shrubs [ 60 ], herring [ 61 ], and cyst nematodes [ 62 ]. To the best of our knowledge, this approach has not been used before for the characterization of temporal changes in the genetic composition of plant populations.…”

Persisting in a glaciated landscape: Pleistocene microrefugia evidenced by the tree wētā Hemideina maori in central South Island, New Zealand

“…Similarly, in North America, coastal and offshore microrefugia including Haida Gwaii (Pruett et al., 2013), Alexander Archipelago (Lucid & Cook, 2004), parts of the Arctic (Waltari & Cook, 2005) and even small pockets within the ice sheets (Marr, Allen, & Hebda, 2008), apparently facilitated species persistence outside major Beringian and Pacific Northwest refugia. In the Southern Hemisphere, microrefugia have been inferred to allow species persistence at sites affected by Pleistocene glaciations in Tasmania (Cliff, Wapstra, & Burridge, 2015; Kreger et al., 2020), Victoria (Bell, Griffin, Hoffmann, & Miller, 2018; Endo et al., 2015; Slatyer et al., 2014) and Patagonia (Breitman, Avila, Sites, & Morando, 2012), evidenced by high regional genetic diversity. In addition to idiosyncratic patterns generated by microrefugia, physiologically distinct lineages can exhibit divergent biogeographic histories under glaciation: temperate–adapted species typically undergo range contraction, whereas cold‐adapted, montane species experience range expansion via down‐slope extension of alpine habitat (DeChaine & Martin, 2004; Trewick, Wallis, & Morgan‐Richards, 2000).…”