An endangered flightless grasshopper with strong genetic structure maintains population genetic variation despite extensive habitat loss

Abstract

Conservation research is dominated by vertebrate examples but the shorter generation times and high local population sizes of invertebrates may lead to very different management strategies, particularly for species with low movement rates. Here we investigate the genetic structure of an endangered flightless grasshopper, Keyacris scurra, which was used in classical evolutionary studies in the 1960s. It had a wide distribution across New South Wales (NSW) and Victoria in pre-European times but has now become threatened because of land clearing for agriculture and other activities. We revisited remnant sites of K. scurra, with populations now restricted to only one area in Victoria and a few small patches in NSW and the Australian Capital Territory (ACT). Using DArtseq to generate SNP markers as well as mtDNA sequence data, we show that the remaining Victorian populations in an isolated valley are genetically distinct from the NSW populations and that all populations tend to be genetically unique, with large F _ST values up to 0.8 being detected for the SNP datasets. We also find that, with one notable exception, the NSW/ACT populations separate genetically into previously described chromosomal races (2n = 15 vs. 2n = 17). Isolation by distance was detected across both the SNP and mtDNA datasets, and there was substantial differentiation within chromosomal races. Genetic diversity as measured by heterozygosity was not correlated with the size of remaining habitat where the populations were found, with high variation present in some remnant cemetery sites. However, inbreeding correlated negatively with estimated habitat size at 25-500 m patch radius. These findings emphasize the importance of small habitat areas in conserving genetic variation in such species with low mobility, and they highlight populations suitable for future translocation efforts.

Keywords: Keyacris; fragmentation; grassland; isolation by distance; morabine; small population area.

FIGURE 1

Map of sites surveyed for molecular variation. These sites encompass most of the current known fragmented distribution of Keyacris scurra. Singletons from two additional sites were included in the molecular survey: a site close to Gundagai (“Gundagai Cemetery”) and a site close to Windellama (“Windellama North”). Chromosomal races based on White (1956) are displayed in black dots (2n = 17) and triangles (2n = 15)

FIGURE 2

Box plots for individual heterozygosity by location (for selected SNPs, all individuals prefiltered to MAC = 1 from data where population with an even number of individuals were sampled, but then computed for all individuals from a population). Note that populations are ordered to match the STRUCTURE analysis below. Gundagai Cemetery and Windellama North are not included here because they are represented by singletons

FIGURE 3

Association between a likelihood model of intact native grassland (S. J. Sinclair and M. D. White, unpublished) at different spatial scales (“buffers”) and observed heterozygosity (left column) or F _IS (right column). Dots reflect individual sites and are presented with correlation coefficients (r) and p values

FIGURE 4

Variation in the COI gene sequence across Keyacris scurra as depicted by a network diagram. The numbers of nucleotide changes are indicated in brackets. The size of the colored areas reflects the number of haplotypes, and branch lengths reflect the number of nucleotide changes. COI, cytochrome oxidase subunit 1

FIGURE 5

STRUCTURE plots for (a) all individuals and (b) even populations at K = 6 (best supported by modified Evanno method)

FIGURE 6

STRUCTURE analysis on all individuals from populations at different K values

FIGURE 7

DAPC of Keyacris scurra individuals with Omeo and Cooma included along the two main linear discriminant (LD) axes (a) and the first and third axes (b) and when these populations are excluded (c) (N = 158, 45 PCs, RMSE 0.043 when all sites included; N = 131, 30 PCs, RMSE = 0.029 when Cooma and Omeo excluded)

FIGURE 8

Pairwise F _ST values for comparisons of sites (excluding those with singletons)

FIGURE 9

Bayesian tree representing individual grasshoppers generated from SNP data with probability support values shown at branch nodes. Note the tight clustering by site location

FIGURE 10

RAxML tree representing individual grasshoppers generated from SNP data with bootstrap support values shown at branch nodes. Note the tight clustering by site location

FIGURE 11

Correlation of geographic distance with F _ST‐derived distance between populations