Phenotypic and genetic divergence in a cold-adapted grasshopper may lead to lineage-specific responses to rapid climate change
Data files
Nov 11, 2024 version files 37.61 KB
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1._Genetic_data.zip
5.48 KB
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2._Morphological_data.zip
16.65 KB
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3._ENM_data.zip
7.93 KB
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README.md
7.54 KB
Abstract
Aim: Species responses to global warming will depend on intraspecific diversity, yet studies of factors governing biogeographic patterns of variability are scarce. Here, we investigate the evolutionary processes underlying genetic and phenotypic diversity in the flightless and cold-adapted grasshopper Sigaus piliferus, and project its suitable space in time.
Location: Te Ika-a-Māui Aotearoa—North Island of New Zealand.
Methods: We used mitochondrial sequences to investigate population connectivity and demographic trends using phylogeographic tools and neutrality statistics. Metric data were used to document phenotypic variation using naïve clustering. We used niche metrics to assess intraspecific niche variation, and niche modelling to investigate suitability under past and future scenarios. Multiple matrix regressions with randomization explored the processes contributing to phenotypic differentiation among grasshopper populations.
Results: Niche models and demographic analyses suggest suitable space for this grasshopper was more restricted during glacial than interglacial stages. Genealogical relationships among ND2 haplotypes revealed a deep north-south split partly concordant with phenotypic and niche variation, suggesting two ecotypes that have mixed during recolonisation of the central volcanic region. Multiple matrix regressions with randomization indicate a link between climate and phenotypic differentiation inferred from leg and pronotum dimensions but not pronotum shape. Niche projections predict severe habitat reduction due to climate warming.
Main conclusions: The current distribution and intraspecific diversity of S. piliferus reflect complex biogeographical scenarios consistent with Quaternary climates and volcanism. Phenotypic divergence appears adaptive. Current levels of genetic and phenotypic variation suggest adaptive potential, yet the pace of anthropogenic warming over the next 50 years could result in small populations that may collapse before adapting. Differences in niche features between diverging intraspecific lineages suggest distinct responses to climate change, and this has implications for prioritising conservation actions and management strategies.
README
README: Phenotypic and genetic divergence in a cold-adapted grasshopper may lead to lineage-specific responses to rapid climate change: Open Source Data
We have submitted the data used for (1) genetic (Genetic data.zip), (2) morphological (Morphological data.zip), and (3) ecological niche modelling (ENM data.zip).
Description of the data and file structure
##1. Genetic data.zip
This dataset consists of a 747 bp alignment of mitochondrial ND2 sequence for 186 individual Sigaus piliferus plus one sequence of Sigaus villosus, which was used as an outgroup in the phylogenetic analysis. Whole genomic DNA was extracted from leg muscle using a solvent-free Proteinase K and salting-out method (Trewick & Morgan-Richards, 2005). Extracted DNA was amplified by PCR for the mitochondrial protein-coding NADH-dehydrogenase 2 (ND2) gene under standard conditions, using the primers HopND2_147F and HopND2_1286R (Carmelet-Rescan et al., 2021). Sequencing reactions used BigDye Terminator v.3.1 (Life Technologies) with signal capture on an ABI-3730xl System (ThermoFisher). DNA sequences were edited and aligned in GENEIOUS vR10 (Kearse et al., 2012), and then exported in Phylip format as Sigaus piliferus.phy. The mtDNA sequences used to generate this file are openly available in Genbank, accession numbers PP277795–PP277981.
#1.1. Sigaus piliferus.phy
Phylip file of the alignment of ND2 partial gene used for the population genetics and phylogenetic analysis. This file consists of 187 lines (rows), one for each sequence in the alignment. Each row consists of a sequence identifier (ID) followed by characters in the sequence (747 bp in this case). The sequnce indentifier (ID) followed a fiexd format: population_geographic region_specimen identifier.
##2. Morphological data.zip
This dataset consists of the two files used for metric and geometric morphometrics of phenotypic variation. For metric analysis we used four non-independent body dimensions (hind femur length, FL; hind femur width, FW; pronotum length, PL; pronotum width, PW) and two ratios (FL/FW and PW/PL) were recorded from 156 adult grasshoppers (n = 100♀, 56♂) using an Olympus SZX7 stereomicroscope with image capture and Olympus cellSens Dimension v1.6 software (Olympus Corporation, Japan). Geometric analysis of pronotum shape used 14 digitalised landmarks on the dorsal perimeter of the pronotum in images from 161 adult grasshoppers (n = 101♀, 60♂) using TPSDIG2 2.29 (Rohlf, 2015). Images were taken using a Canon EOS 600D with EF100 mm f2.8 USM macro lens (Canon Inc., Japan) mounted on a vertical stand (Kaiser Fototechnik, Germany). Only females were analysed hereafter due to better sample size and more homogeneous geographic sampling compared to males.
#2.1 body shape.TPS
Coordinates and scale of the landmarks used for geometric morphometrics analysis. This file consists of 100 entries, one for each image. The first line (row) indicates the number of landmarks (14 in this case), following for 14 lines containing the pairs of coordinates for each landmark. The next line (IMAGE) indicates the name of the image in this case denoting the specimen identifier (ID), followed for a line including specimen information (ID): specimen ID, sex, and genetic lineage based on genetic analyses. The last row indicates the image scale.
LM=14
1355.00000 2173.00000
1410.00000 2650.00000
2019.00000 2508.00000
2342.00000 2436.00000
2535.00000 2379.00000
2899.00000 2356.00000
2942.00000 2015.00000
2895.00000 1682.00000
2527.00000 1655.00000
2336.00000 1622.00000
2013.00000 1534.00000
1402.00000 1384.00000
1351.00000 1865.00000
1460.00000 2037.00000
IMAGE=GH002.JPG
ID=GH002-F-North
SCALE=0.005263
#2.2 body size.xls
Linear dimensions used for traditional morphometrics analysis. This file consists of 156 entries (n = 100♀, 56♂), yet only females were analysed. For each entry, there are 13 rows:
Code: specimen identifier (ID)
Femur_length: femur length (mm)
Femur_width: femur width (mm)
Pronotum_length: pronotum length (mm)
Pronotum_width: pronotum width (mm)
Latitude: absolute latitude (degrees)
Longitude: absolute longitude (degrees)
Elevation: elevation (m)
Population: population name
Region: geographic region
Year: collection year
Sex: male (M) or female (F)
Lineage: North or South
##3. ENM data.zip
This dataset consists of a presence-absence matrix (geodetic datum WGS84) including data for 14 related, endemic New Zealand grasshopper species, spanning 1967 to 2016 (Koot et al., 2022), plus recent sample collections and verified, high resolution observations (uncertainty <1km2) from iNaturalist NZ. We also included target-group absences (Mateo et al., 2010) consisting of sites where sampling effort has produced other Orthoptera (Gryllidae and Tettigoniidae), but not S. piliferus. Duplicate records were removed ensuring one datum per pixel (i.e. ~1 km2 habitat area). The resulting database consisted of 1,188 site records, including 1,053 absences and 135 presences, representing the realised niche of S. piliferus.
#3.1. Sigaus piliferus.csv
Presence/absence data used for niche modelling and analysis. This file consists of 1,188 entries, and for each entry, there are 3 rows:
Latitude: latitude (degrees)
Longitude: longitude (degrees)
Spiliferus: presence (1), absence (0)
As potential niche proxies we used 19 bioclimatic layers from WorldClim v1.4 for five periods (MIROC-ESM and NCAR-CCSM climate models): last interglacial at ∼120–140 kyr (LIG), last glacial maximum at ~28 kyr (LGM), mid-Holocene at ∼6 kyr (MH), current (1960–1990), and future (2061–2080). We projected two future scenarios with mean temperature increases of 1.4 °C (RCP4.5) and 3.0 °C (RCP8.5) in New Zealand by 2090 (Ministry for the Environment, 2018). Layer files were at 30 arc-seconds resolution (~1 km2), except LGM which was at 2.5 arc minutes (~5 km2). The climate data for ecological niche modelling and niche analyses are freely available at https://www.worldclim.org/data/worldclim21.html.
##4. References
Trewick, S. A., & Morgan‐Richards, M. (2005). After the deluge: mitochondrial DNA indicates Miocene radiation and Pliocene adaptation of tree and giant weta (Orthoptera: Anostostomatidae). Journal of Biogeography, 32(2), 295-309.
Carmelet‐Rescan, D., Morgan‐Richards, M., Koot, E. M., & Trewick, S. A. (2021). Climate and ice in the last glacial maximum explain patterns of isolation by distance inferred for alpine grasshoppers. Insect Conservation and Diversity, 14(5), 568-581.
Kearse, M., Moir, R., Wilson, A., Stones-Havas, S., Cheung, M., Sturrock, S., ... & Thierer, T. (2012). Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics, 28(12), 1647–1649.
Rohlf, F. (2015). The Tps series of software. Hystrix, the Italian Journal of Mammalogy, 26, 1–4.
Koot, E. M., Morgan-Richards, M., Trewick, S. A. (2022). Climate change and alpine adapted insects: Modelling environmental envelopes of a grasshopper radiation. Royal Society Open Science, 9: 211596.
Mateo, R. G., Croat, T. B., Felicísimo, A. M. & Muñoz, J. (2010). Profile or group discriminative techniques? Generating reliable species distribution models using pseudo-absences and target-group absences from natural history collections. Diversity and Distributions, 16(1), 84–94.