Recent range expansion in Australian hummock grasses (Triodia) inferred using genotyping-by-sequencing

Benjamin M. Anderson, Kevin R. Thiele, Pauline F. Grierson, Siegfried L. Krauss, Paul G. Nevill, Ian D. Small, Xiao Zhong, Matthew D. Barrett

Research output: Contribution to journalArticle

Abstract

The Australian arid zone (AAZ) has undergone aridification and the formation of vast sandy deserts since the mid-Miocene. Studies on AAZ organisms, particularly animals, have shown patterns of mesic ancestry, persistence in rocky refugia and range expansions in arid lineages. There has been limited molecular investigation of plants in the AAZ, particularly of taxa that arrived in Australia after the onset of aridification. Here we investigate populations of the widespread AAZ grass Triodia basedowii to determine whether there is evidence for a recent range expansion, and if so, its source and direction. We also undertake a dating analysis for the species complex to which T. basedowii belongs, in order to place its diversification in relation to changes in AAZ climate and landscapes. We analyse a genomic single nucleotide polymorphism data set from 17 populations of T. basedowii in a recently developed approach for detecting the signal and likely origin of a range expansion. We also use alignments from existing and newly sequenced plastomes from across Poaceae for analysis in BEAST to construct fossil-calibrated phylogenies. Across a range of sampling parameters and outgroups, we detected a consistent signal of westward expansion for T. basedowii, originating in central or eastern Australia. Divergence time estimation indicates that Triodia began to diversify in the late Miocene (crown 7.0-8.8 million years (Ma)), and the T. basedowii complex began to radiate during the Pleistocene (crown 1.4-2.0 Ma). This evidence for range expansion in an arid-adapted plant is consistent with similar patterns in AAZ animals and likely reflects a general response to the opening of new habitat during aridification. Radiation of the T. basedowii complex through the Pleistocene has been associated with preferences for different substrates, providing an explanation why only one lineage is widespread across sandy deserts.

Much of Australia is covered by an arid zone that has developed over the last 15 million years (Ma). The unique flora that inhabits that arid zone includes plants that have responded differently (expanding or contracting their ranges) to climate and landscape changes. Here we show that one widespread desert grass, Triodia basedowii, has recently (within the last 2 Ma) expanded across the arid zone. Surprisingly, we find evidence of an expansion origin in central or eastern Australia, while the bulk of the diversity in the group to which T.basedowii belongs exists in western Australia.

Original languageEnglish
Article number017
Number of pages14
JournalAOB Plants
Volume11
Issue number2
DOIs
Publication statusPublished - Apr 2019

Cite this

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title = "Recent range expansion in Australian hummock grasses (Triodia) inferred using genotyping-by-sequencing",
abstract = "The Australian arid zone (AAZ) has undergone aridification and the formation of vast sandy deserts since the mid-Miocene. Studies on AAZ organisms, particularly animals, have shown patterns of mesic ancestry, persistence in rocky refugia and range expansions in arid lineages. There has been limited molecular investigation of plants in the AAZ, particularly of taxa that arrived in Australia after the onset of aridification. Here we investigate populations of the widespread AAZ grass Triodia basedowii to determine whether there is evidence for a recent range expansion, and if so, its source and direction. We also undertake a dating analysis for the species complex to which T. basedowii belongs, in order to place its diversification in relation to changes in AAZ climate and landscapes. We analyse a genomic single nucleotide polymorphism data set from 17 populations of T. basedowii in a recently developed approach for detecting the signal and likely origin of a range expansion. We also use alignments from existing and newly sequenced plastomes from across Poaceae for analysis in BEAST to construct fossil-calibrated phylogenies. Across a range of sampling parameters and outgroups, we detected a consistent signal of westward expansion for T. basedowii, originating in central or eastern Australia. Divergence time estimation indicates that Triodia began to diversify in the late Miocene (crown 7.0-8.8 million years (Ma)), and the T. basedowii complex began to radiate during the Pleistocene (crown 1.4-2.0 Ma). This evidence for range expansion in an arid-adapted plant is consistent with similar patterns in AAZ animals and likely reflects a general response to the opening of new habitat during aridification. Radiation of the T. basedowii complex through the Pleistocene has been associated with preferences for different substrates, providing an explanation why only one lineage is widespread across sandy deserts.Much of Australia is covered by an arid zone that has developed over the last 15 million years (Ma). The unique flora that inhabits that arid zone includes plants that have responded differently (expanding or contracting their ranges) to climate and landscape changes. Here we show that one widespread desert grass, Triodia basedowii, has recently (within the last 2 Ma) expanded across the arid zone. Surprisingly, we find evidence of an expansion origin in central or eastern Australia, while the bulk of the diversity in the group to which T.basedowii belongs exists in western Australia.",
keywords = "Arid zone, Australia, biogeography, chloroplast, divergence dating, genotyping-by-sequencing, Poaceae, range expansion, SNPs, Triodia basedowii species complex, ARID ZONE, HETERONOTIA-BINOEI, SPECIES COMPLEX, DIVERSIFICATION, EVOLUTION, CLIMATE, HISTORY, LIZARD, BIOGEOGRAPHY, PLIOCENE",
author = "Anderson, {Benjamin M.} and Thiele, {Kevin R.} and Grierson, {Pauline F.} and Krauss, {Siegfried L.} and Nevill, {Paul G.} and Small, {Ian D.} and Xiao Zhong and Barrett, {Matthew D.}",
year = "2019",
month = "4",
doi = "10.1093/aobpla/plz017",
language = "English",
volume = "11",
journal = "Annals of Botany Plants",
issn = "2041-2851",
publisher = "Oxford University Press",
number = "2",

}

Recent range expansion in Australian hummock grasses (Triodia) inferred using genotyping-by-sequencing. / Anderson, Benjamin M.; Thiele, Kevin R.; Grierson, Pauline F.; Krauss, Siegfried L.; Nevill, Paul G.; Small, Ian D.; Zhong, Xiao; Barrett, Matthew D.

In: AOB Plants, Vol. 11, No. 2, 017, 04.2019.

Research output: Contribution to journalArticle

TY - JOUR

T1 - Recent range expansion in Australian hummock grasses (Triodia) inferred using genotyping-by-sequencing

AU - Anderson, Benjamin M.

AU - Thiele, Kevin R.

AU - Grierson, Pauline F.

AU - Krauss, Siegfried L.

AU - Nevill, Paul G.

AU - Small, Ian D.

AU - Zhong, Xiao

AU - Barrett, Matthew D.

PY - 2019/4

Y1 - 2019/4

N2 - The Australian arid zone (AAZ) has undergone aridification and the formation of vast sandy deserts since the mid-Miocene. Studies on AAZ organisms, particularly animals, have shown patterns of mesic ancestry, persistence in rocky refugia and range expansions in arid lineages. There has been limited molecular investigation of plants in the AAZ, particularly of taxa that arrived in Australia after the onset of aridification. Here we investigate populations of the widespread AAZ grass Triodia basedowii to determine whether there is evidence for a recent range expansion, and if so, its source and direction. We also undertake a dating analysis for the species complex to which T. basedowii belongs, in order to place its diversification in relation to changes in AAZ climate and landscapes. We analyse a genomic single nucleotide polymorphism data set from 17 populations of T. basedowii in a recently developed approach for detecting the signal and likely origin of a range expansion. We also use alignments from existing and newly sequenced plastomes from across Poaceae for analysis in BEAST to construct fossil-calibrated phylogenies. Across a range of sampling parameters and outgroups, we detected a consistent signal of westward expansion for T. basedowii, originating in central or eastern Australia. Divergence time estimation indicates that Triodia began to diversify in the late Miocene (crown 7.0-8.8 million years (Ma)), and the T. basedowii complex began to radiate during the Pleistocene (crown 1.4-2.0 Ma). This evidence for range expansion in an arid-adapted plant is consistent with similar patterns in AAZ animals and likely reflects a general response to the opening of new habitat during aridification. Radiation of the T. basedowii complex through the Pleistocene has been associated with preferences for different substrates, providing an explanation why only one lineage is widespread across sandy deserts.Much of Australia is covered by an arid zone that has developed over the last 15 million years (Ma). The unique flora that inhabits that arid zone includes plants that have responded differently (expanding or contracting their ranges) to climate and landscape changes. Here we show that one widespread desert grass, Triodia basedowii, has recently (within the last 2 Ma) expanded across the arid zone. Surprisingly, we find evidence of an expansion origin in central or eastern Australia, while the bulk of the diversity in the group to which T.basedowii belongs exists in western Australia.

AB - The Australian arid zone (AAZ) has undergone aridification and the formation of vast sandy deserts since the mid-Miocene. Studies on AAZ organisms, particularly animals, have shown patterns of mesic ancestry, persistence in rocky refugia and range expansions in arid lineages. There has been limited molecular investigation of plants in the AAZ, particularly of taxa that arrived in Australia after the onset of aridification. Here we investigate populations of the widespread AAZ grass Triodia basedowii to determine whether there is evidence for a recent range expansion, and if so, its source and direction. We also undertake a dating analysis for the species complex to which T. basedowii belongs, in order to place its diversification in relation to changes in AAZ climate and landscapes. We analyse a genomic single nucleotide polymorphism data set from 17 populations of T. basedowii in a recently developed approach for detecting the signal and likely origin of a range expansion. We also use alignments from existing and newly sequenced plastomes from across Poaceae for analysis in BEAST to construct fossil-calibrated phylogenies. Across a range of sampling parameters and outgroups, we detected a consistent signal of westward expansion for T. basedowii, originating in central or eastern Australia. Divergence time estimation indicates that Triodia began to diversify in the late Miocene (crown 7.0-8.8 million years (Ma)), and the T. basedowii complex began to radiate during the Pleistocene (crown 1.4-2.0 Ma). This evidence for range expansion in an arid-adapted plant is consistent with similar patterns in AAZ animals and likely reflects a general response to the opening of new habitat during aridification. Radiation of the T. basedowii complex through the Pleistocene has been associated with preferences for different substrates, providing an explanation why only one lineage is widespread across sandy deserts.Much of Australia is covered by an arid zone that has developed over the last 15 million years (Ma). The unique flora that inhabits that arid zone includes plants that have responded differently (expanding or contracting their ranges) to climate and landscape changes. Here we show that one widespread desert grass, Triodia basedowii, has recently (within the last 2 Ma) expanded across the arid zone. Surprisingly, we find evidence of an expansion origin in central or eastern Australia, while the bulk of the diversity in the group to which T.basedowii belongs exists in western Australia.

KW - Arid zone

KW - Australia

KW - biogeography

KW - chloroplast

KW - divergence dating

KW - genotyping-by-sequencing

KW - Poaceae

KW - range expansion

KW - SNPs

KW - Triodia basedowii species complex

KW - ARID ZONE

KW - HETERONOTIA-BINOEI

KW - SPECIES COMPLEX

KW - DIVERSIFICATION

KW - EVOLUTION

KW - CLIMATE

KW - HISTORY

KW - LIZARD

KW - BIOGEOGRAPHY

KW - PLIOCENE

U2 - 10.1093/aobpla/plz017

DO - 10.1093/aobpla/plz017

M3 - Article

VL - 11

JO - Annals of Botany Plants

JF - Annals of Botany Plants

SN - 2041-2851

IS - 2

M1 - 017

ER -