Dataset Information

Genomic impact of severe population decline in a nomadic songbird

ABSTRACT: Uncovering the population genetic histories of non-model organisms is increasingly possible through advances in next generation sequencing and DNA sampling of museum specimens. This new information can inform conservation of threatened species, particularly those for which historical and contemporary population data are unavailable or challenging to obtain. The critically endangered, nomadic regent honeyeater Anthochaera phrygia was abundant and widespread throughout south-eastern Australia prior to a rapid population decline and range contraction since the 1970s. A current estimated population of 250?400 individuals is distributed sparsely across 600,000 km2 from northern Victoria to southern Queensland. Using hybridization RAD (hyRAD) techniques, we obtained 3,524 Single Nucleotide Polymorphisms from 64 museum specimens (date 1879?1960), 102 `recent? (1989?2012) and 52 `current? (2015?2016) wild birds sampled throughout the historical and contemporary range. We aimed to estimate population genetic structure, genetic diversity and population size of the regent honeyeater prior to its rapid decline. We then assessed the impact of the decline on recent and current population size, structure and genetic diversity. We found low population structure in the remaining regent honeyeater population, which appears to be a consequence of the species? life-history, rather than population decline and range contraction. Population decline has led to minimal but detectable loss of genetic diversity since the 1980?s. Capacity to quantify the overall magnitude of both genetic diversity loss and population decline was limited by the poorer quality of genomic data derived from museum specimens. We discuss the implications for genetic management of endangered mobile species and enhancing the value of museum specimens in population genomic studies.

INSTRUMENT(S): Illumina HiSeq 2500

ORGANISM(S): Anthochaera Phrygia

SUBMITTER: Fenner School of Environment & Society, The Australian National University

PROVIDER: PRJEB33704 | EVA | 2019-11-07

REPOSITORIES: EVA

ACCESS DATA

Dataset's files

Source:

			Action	DRS
	hyRAD_RegentHE2.accessioned.vcf.gz	Vcf
	hyRAD_RegentHE2.accessioned.vcf.gz.csi	Vcf
	hyRAD_RegentHE2.accessioned.vcf.gz.tbi	Vcf
	hyRAD_RegentHE2.vcf.gz	Vcf
	hyRAD_RegentHE2.vcf.gz.tbi	Vcf

Items per page:

1 - 5 of 5

Similar Datasets

Project description:We used custom Nimblegen microarrays representing whole-larval transcriptomes for two species (Erynnis propertius [this submission] and Papilio zelicaon [submitted seperately]) to assess gene expression differences affecting tolerance to climatic regimes. Many individuals were sourced from populations from the northern periphery and center of the species' (shared) range; these were each divided into groups treated under peripheral and central climate regimes, resulting in 4 experimental groups for each species (Peripheral Source, Peripheral treatment; Peripheral Source, Central Treatment; Central Source, Peripheral Treatment; Central Source, Central Treatment). Using technical microarray replicates allowed us to use ANOVA to identify genes whose expression may underlie local adaptation to climate (i.e., those showing an interaction term between source and population). Abstract: Population differences may determine geographic range shifts and adaptive evolution under climate change. Local adaptation in peripheral populations could preclude or slow range expansions, and populations with different genetic make-up could have distinct trajectories that produce complex spatial patterns of population change. To investigate the genetic extent of local responses to climate change, we exposed poleward-periphery and central populations of two Lepidoptera to reciprocal, common-garden climatic conditions and compared whole-transcriptome expression. We found significant expression differences between populations in both species. In addition, several hundred genes including genes involved in energy metabolism and oxidative stress responded in a localized fashion in the species that exhibits greater population structure and local adaptation. Expression levels of these genes are most divergent in the same environment in which we previously detected phenotypic divergence in metabolism. By contrast, we found no localized genes in the species with higher gene flow, reflecting the lack of previously observed local adaptation. These results suggest that population differences do not generalize easily, even for related species living in the same climate, but some taxa deserve population-level consideration when predicting the effects of climate change.

Project description:We used custom Nimblegen microarrays representing whole-larval transcriptomes for two species (Papilio zelicaon [this submission] and Erynnis propertius [submitted seperately]) to assess gene expression differences affecting tolerance to climatic regimes. Many individuals were sourced from populations from the northern periphery and center of the species' (shared) range; these were each divided into groups treated under peripheral and central climate regimes, resulting in 4 experimental groups for each species (Peripheral Source, Peripheral treatment; Peripheral Source, Central Treatment; Central Source, Peripheral Treatment; Central Source, Central Treatment). Using technical microarray replicates allowed us to use ANOVA to identify genes whose expression may underlie local adaptation to climate (i.e., those showing an interaction term between source and population). Abstract: Population differences may determine geographic range shifts and adaptive evolution under climate change. Local adaptation in peripheral populations could preclude or slow range expansions, and populations with different genetic make-up could have distinct trajectories that produce complex spatial patterns of population change. To investigate the genetic extent of local responses to climate change, we exposed poleward-periphery and central populations of two Lepidoptera to reciprocal, common-garden climatic conditions and compared whole-transcriptome expression. We found significant expression differences between populations in both species. In addition, several hundred genes including genes involved in energy metabolism and oxidative stress responded in a localized fashion in the species that exhibits greater population structure and local adaptation. Expression levels of these genes are most divergent in the same environment in which we previously detected phenotypic divergence in metabolism. By contrast, we found no localized genes in the species with higher gene flow, reflecting the lack of previously observed local adaptation. These results suggest that population differences do not generalize easily, even for related species living in the same climate, but some taxa deserve population-level consideration when predicting the effects of climate change.

Dataset Information

Genomic impact of severe population decline in a nomadic songbird

Dataset's files

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets