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Fluctuating fortunes: genomes and habitat reconstructions reveal global climate-mediated changes in bats' genetic diversity.

ABSTRACT: Over the last approximately 2.6 Myr, Earth's climate has been dominated by cyclical ice ages that have profoundly affected species' population sizes, but the impact of impending anthropogenic climate change on species' extinction potential remains a worrying problem. We investigated 11 bat species from different taxonomic, ecological and geographical backgrounds using combined information from palaeoclimatic habitat reconstructions and genomes to analyse biotic impacts of historic climate change. We discover tightly correlated fluctuations between species' historic distribution and effective population size, identify frugivores as particularly susceptible to global warming, pinpoint large insectivores as having overall low effective population size and flag the onset of the Holocene (approx. 10-12 000 years ago) as the period with the generally lowest effective population sizes across the last approximately 1 Myr. Our study shows that combining genomic and palaeoclimatological approaches reveals effects of climatic shifts on genetic diversity and may help predict impacts of future climate change.

SUBMITTER: Chattopadhyay B

PROVIDER: S-EPMC6784725 | biostudies-literature | 2019 Sep

REPOSITORIES: biostudies-literature

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Fluctuating fortunes: genomes and habitat reconstructions reveal global climate-mediated changes in bats' genetic diversity.

Chattopadhyay Balaji B Garg Kritika M KM Ray Rajasri R Rheindt Frank E FE

Proceedings. Biological sciences 20190918 1911

Over the last approximately 2.6 Myr, Earth's climate has been dominated by cyclical ice ages that have profoundly affected species' population sizes, but the impact of impending anthropogenic climate change on species' extinction potential remains a worrying problem. We investigated 11 bat species from different taxonomic, ecological and geographical backgrounds using combined information from palaeoclimatic habitat reconstructions and genomes to analyse biotic impacts of historic climate change ...[more]

PMID: 31530139

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Project description:Effective management decisions depend on knowledge of species distribution and habitat use. Maps generated from species distribution models are important in predicting previously unknown occurrences of protected species. However, if populations are seasonally dynamic or locally adapted, failing to consider population level differences could lead to erroneous determinations of occurrence probability and ineffective management. The study goal was to model the distribution of a species of special concern, Townsend's big-eared bats (Corynorhinus townsendii), in California. We incorporate seasonal and spatial differences to estimate the distribution under current and future climate conditions. We built species distribution models using all records from statewide roost surveys and by subsetting data to seasonal colonies, representing different phenological stages, and to Environmental Protection Agency Level III Ecoregions to understand how environmental needs vary based on these factors. We projected species' distribution for 2061-2080 in response to low and high emissions scenarios and calculated the expected range shifts. The estimated distribution differed between the combined (full dataset) and phenologically explicit models, while ecoregion-specific models were largely congruent with the combined model. Across the majority of models, precipitation was the most important variable predicting the presence of C. townsendii roosts. Under future climate scenarios, distribution of C. townsendii is expected to contract throughout the state, however suitable areas will expand within some ecoregions. Comparison of phenologically explicit models with combined models indicates the combined models better predict the extent of the known range of C. townsendii in California. However, life-history-explicit models aid in understanding of different environmental needs and distribution of their major phenological stages. Differences between ecoregion-specific and statewide predictions of habitat contractions highlight the need to consider regional variation when forecasting species' responses to climate change. These models can aid in directing seasonally explicit surveys and predicting regions most vulnerable under future climate conditions.

Project description:BACKGROUND: A genome-wide assessment of nucleotide diversity in a polyploid species must minimize the inclusion of homoeologous sequences into diversity estimates and reliably allocate individual haplotypes into their respective genomes. The same requirements complicate the development and deployment of single nucleotide polymorphism (SNP) markers in polyploid species. We report here a strategy that satisfies these requirements and deploy it in the sequencing of genes in cultivated hexaploid wheat (Triticum aestivum, genomes AABBDD) and wild tetraploid wheat (Triticum turgidum ssp. dicoccoides, genomes AABB) from the putative site of wheat domestication in Turkey. Data are used to assess the distribution of diversity among and within wheat genomes and to develop a panel of SNP markers for polyploid wheat. RESULTS: Nucleotide diversity was estimated in 2114 wheat genes and was similar between the A and B genomes and reduced in the D genome. Within a genome, diversity was diminished on some chromosomes. Low diversity was always accompanied by an excess of rare alleles. A total of 5,471 SNPs was discovered in 1791 wheat genes. Totals of 1,271, 1,218, and 2,203 SNPs were discovered in 488, 463, and 641 genes of wheat putative diploid ancestors, T. urartu, Aegilops speltoides, and Ae. tauschii, respectively. A public database containing genome-specific primers, SNPs, and other information was constructed. A total of 987 genes with nucleotide diversity estimated in one or more of the wheat genomes was placed on an Ae. tauschii genetic map, and the map was superimposed on wheat deletion-bin maps. The agreement between the maps was assessed. CONCLUSIONS: In a young polyploid, exemplified by T. aestivum, ancestral species are the primary source of genetic diversity. Low effective recombination due to self-pollination and a genetic mechanism precluding homoeologous chromosome pairing during polyploid meiosis can lead to the loss of diversity from large chromosomal regions. The net effect of these factors in T. aestivum is large variation in diversity among genomes and chromosomes, which impacts the development of SNP markers and their practical utility. Accumulation of new mutations in older polyploid species, such as wild emmer, results in increased diversity and its more uniform distribution across the genome.

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Fluctuating fortunes: genomes and habitat reconstructions reveal global climate-mediated changes in bats' genetic diversity.

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Fluctuating fortunes: genomes and habitat reconstructions reveal global climate-mediated changes in bats' genetic diversity.

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