Complex Population Structure Research Articles

Otolith phenotypic variability of the blue jack mackerel, Trachurus picturatus, from the Canary Islands (NE Atlantic): Implications in its population dynamic

Studies have described the presence of different population units of blue jack mackerel, Trachurus picturatus, in the NE Atlantic region. However, the hypothesis of several populations has been subtly questioned due to the high similarity in the otolith shape among some regions. It suggests the possibility of migrations processes connecting them, especially between Madeira, the Canary Islands and the African coast, being the Canary Islands the region with higher potential of mixing due to the oceanographic conditions. In order to explore this hypothesis, we quantified the phenotypic variability in the otolith contour of the blue jack mackerel from Canary Islands using wavelets as mathematical descriptor. Our findings revealed the presence of three otolith phenotypes (M1, M2 and M3) in similar proportions. They were not linked to sex, age and size, but showed temporal variations associated with spawning, recruitment and feeding seasons. The best model to explain the population structure of T. picturatus in the Canary waters was based on local migration triangles and the ‘contingent theory’, where migrants and residents compose the population. In addition, we estimated different somatic growth parameters linked to these phenotypes. These results suggest a complex population structure in the region with possibility of connectivity with the closest populations inhabiting the Madeira archipelago and the African coast. However, future studies are necessary including the whole Atlantic distribution of the species, with special attention to the seasonal variations in the frequency of these phenotypes to clarify the intraspecific polymorphism and the migratory processes.

Ecological flow process acknowledging different spawning patterns in the Songhua River

Based on the complex population structure of fish species in Songhua River, this paper broke through the present method modeling by the single target species and introduced a developed approach classified by different spawning habits to evaluate ecological flow. Three main spawning periods and two spawning types were respectively analyzed combining with biographical information. For the characteristic of abundant branching channel and wide floodplain in study area, MIKE21 hydrodynamic model was applied to simulate hydrological condition. Combing the habitat preference curves and hydrodynamic results, the composite suitability index for the study reach was attained. At the same time, the lasting time of fish incubation was used to suggest the flow duration. At last, this paper put forward the optimal discharge, flow duration, occurrence time and frequency in April, May and June-July respectively. Using this result, the ecological flow process can effectively support to the management strategies for rational allocation of water resources.

The problems of genetic support of dividing the black kite (Milvus migrans) into subspecies

The black kite Milvus migrans is a common bird of prey demonstrating remarkable ecological plasticity. It inhabits a variety of habitats and is an increasingly synanthropic species. The black kite is widespread in Eurasia, Africa, Australia and adjacent islands. Palearctic kites migrate to Africa, India and China in winter, but kites of Africa and Australia are partly sedentary and partly seasonal migrants. The wide range and high mobility are the reasons of a complex population structure of the black kite. Commonly five to seven M. migrans subspecies are distinguished, each of which is widespread over extensive areas and has more or less an apparent phenotype. Recently, studies of genetic differences between black kite populations started to emerge. On the grounds of earlier studies of mitochondrial and nuclear genes of this species, we check whether there is a genetic support for separation of the black kite subspecies. Recent studies of some mitochondrial loci substantiate the recognition of at least the European (M. m. migrans), Asian (M. m. lineatus and M. m. govinda), African (M. m. aegyptius and M. m. parasitus), and Australian (M. m. affinis) black kite subspecies. Furthermore, the mitochondrial haplotype difference suggests that the African yellow-billed kite, including M. m. aegyptius and M. m. parasitus, should be a separate species as already proposed, or even two separate species.

Size-dependent change in body shape and its possible ecological role in the Patagonian squid (Doryteuthis gahi) in the Southwest Atlantic

Cephalopods are a versatile group with several mechanisms in place to ensure the success of future generations. The Patagonian long-finned squid (Doryteuthis gahi) populations on the southern Patagonian shelf are believed to be genetically homogenous, but the mechanisms connecting them geographically and temporally are unresolved. Individual growth is highly variable within cephalopod populations and is likely to affect individual patterns of migration and, thus, population connectivity as a whole. Therefore, this study aimed to make inferences about population structure by analysing the size at which individuals were mature and aimed to describe the intrapopulation growth (allometric) trajectories of body shape, using landmark-based geometric morphometric techniques to describe phenotypes. Samples were collected from June 1999 to November 2017 around 52°S and 58°W. Smoothing curves from binomial generalised additive models (GAMs) suggested two size modes of maturity in females and one or multiple modes in males dependent on year and season. There was a gradual elongation of the mantle and an increase in the relative fin size throughout ontogeny. Shape scores from geometric morphometric shape coordinates revealed a continuous non-linear allometric trajectory with a significantly different slope angle for males exceeding 20.1 cm dorsal mantle length (DML). At the extreme of this continuum, the largest ‘super-bull’ form had a substantially more elongated body shape, a heavier fin and a larger fin area compared to the rest of the population, a body shape associated with enhanced swimming performance which may help to maintain population connectivity. The prevalence of these rare super-bulls in the fishery varied widely between years, suggestive of phenotypic plasticity. This study provides evidence that the D. gahi population on the southern Patagonian shelf has a complex population structure with high intraspecific variation.

High-resolution population structure and runs of homozygosity reveal the genetic architecture of complex traits in the Lipizzan horse

BackgroundThe sample ascertainment bias due to complex population structures remains a major challenge in genome-wide investigations of complex traits. In this study we derived the high-resolution population structure and levels of autozygosity of 377 Lipizzan horses originating from five different European stud farms utilizing the SNP genotype information of the high density 700 k Affymetrix Axiom™ Equine genotyping array. Scanning the genome for overlapping runs of homozygosity (ROH) shared by more than 50% of horses, we identified homozygous regions (ROH islands) in order to investigate the gene content of those candidate regions by gene ontology and enrichment analyses.ResultsThe high-resolution population network approach revealed well-defined substructures according to the origin of the horses (Austria, Slovakia, Croatia and Hungary). The highest mean genome coverage of ROH (SROH) was identified in the Austrian (SROH = 342.9), followed by Croatian (SROH = 214.7), Slovakian (SROH = 205.1) and Hungarian (SROH = 171.5) subpopulations. ROH island analysis revealed five common islands on ECA11 and ECA14, hereby confirming a closer genetic relationship between the Hungarian and Croatian as well as between the Austrian and Slovakian samples. Private islands were detected for the Hungarian and the Austrian Lipizzan subpopulations. All subpopulations shared a homozygous region on ECA11, nearly identical in position and length containing among other genes the homeobox-B cluster, which was also significantly (p < 0.001) highlighted by enrichment analysis. Gene ontology terms were mostly related to biological processes involved in embryonic morphogenesis and anterior/posterior specification. Around the STX17 gene (causative for greying), we identified a ROH island harbouring the genes NR4A3, STX17, ERP44 and INVS. Within further islands on ECA14, ECA16 and ECA20 we detected the genes SPRY4, NDFIP1, IMPDH2, HSP90AB1, whereas SPRY4 and HSP90AB1 are involved in melanoma metastasis and survival rate of melanoma patients in humans.ConclusionsWe demonstrated that the assessment of high-resolution population structures within one single breed supports the downstream genetic analyses (e.g. the identification of ROH islands). By means of ROH island analyses, we identified the genes SPRY4, NDFIP1, IMPDH2, HSP90AB1, which might play an important role for further studies on equine melanoma. Furthermore, our results highlighted the impact of the homeobox-A and B cluster involved in morphogenesis of Lipizzan horses.

Tree-sequence recording in SLiM opens new horizons for forward-time simulation of whole genomes.

There is an increasing demand for evolutionary models to incorporate relatively realistic dynamics, ranging from selection at many genomic sites to complex demography, population structure, and ecological interactions. Such models can generally be implemented as individual-based forward simulations, but the large computational overhead of these models often makes simulation of whole chromosome sequences in large populations infeasible. This situation presents an important obstacle to the field that requires conceptual advances to overcome. The recently developed tree-sequence recording method (Kelleher, Thornton, Ashander, & Ralph, 2018), which stores the genealogical history of all genomes in the simulated population, could provide such an advance. This method has several benefits: (1) it allows neutral mutations to be omitted entirely from forward-time simulations and added later, thereby dramatically improving computational efficiency; (2) it allows neutral burn-in to be constructed extremely efficiently after the fact, using "recapitation"; (3) it allows direct examination and analysis of the genealogical trees along the genome; and (4) it provides a compact representation of a population's genealogy that can be analysed in Python using the msprime package. We have implemented the tree-sequence recording method in SLiM 3 (a free, open-source evolutionary simulation software package) and extended it to allow the recording of non-neutral mutations, greatly broadening the utility of this method. To demonstrate the versatility and performance of this approach, we showcase several practical applications that would have been beyond the reach of previously existing methods, opening up new horizons for the modelling and exploration of evolutionary processes.

Evolutionary epidemiology models to predict the dynamics of antibiotic resistance.

The evolution of resistance to antibiotics is a major public health problem and an example of rapid adaptation under natural selection by antibiotics. The dynamics of antibiotic resistance within and between hosts can be understood in the light of mathematical models that describe the epidemiology and evolution of the bacterial population. “Between‐host” models describe the spread of resistance in the host community, and in more specific settings such as hospitalized hosts (treated by antibiotics at a high rate), or farm animals. These models make predictions on the best strategies to limit the spread of resistance, such as reducing transmission or adapting the prescription of several antibiotics. Models can be fitted to epidemiological data in the context of intensive care units or hospitals to predict the impact of interventions on resistance. It has proven harder to explain the dynamics of resistance in the community at large, in particular because models often do not reproduce the observed coexistence of drug‐sensitive and drug‐resistant strains. “Within‐host” models describe the evolution of resistance within the treated host. They show that the risk of resistance emergence is maximal at an intermediate antibiotic dose, and some models successfully explain experimental data. New models that include the complex host population structure, the interaction between resistance‐determining loci and other loci, or integrating the within‐ and between‐host levels will allow better interpretation of epidemiological and genomic data from common pathogens and better prediction of the evolution of resistance.

Phylogeography of Asian sockeye salmon (Oncorhynchus nerka) based on the analysis of mtDNA D-loop polymorphism

Phylogeography of Asian sockeye salmon (Oncorhynchus nerka) based on the analysis of mtDNA D-loop polymorphism

Linking genes with ecological strategies in Arabidopsis thaliana.

Arabidopsis thaliana is the most prominent model system in plant molecular biology and genetics. Although its ecology was initially neglected, collections of various genotypes revealed a complex population structure, with high levels of genetic diversity and substantial levels of phenotypic variation. This helped identify the genes and gene pathways mediating phenotypic change. Population genetics studies further demonstrated that this variation generally contributes to local adaptation. Here, we review evidence showing that traits affecting plant life history, growth rate, and stress reactions are not only locally adapted, they also often co-vary. Co-variation between these traits indicates that they evolve as trait syndromes, and reveals the ecological diversification that took place within A. thaliana. We argue that examining traits and the gene that control them within the context of global summary schemes that describe major ecological strategies will contribute to resolve important questions in both molecular biology and ecology.

Adult-mediated connectivity and spatial population structure of sardine in the Bay of Biscay and Iberian coast

This work investigated adult-mediated connectivity and spatial population structure of sardine in the European Atlantic waters. The spatial and temporal progress of cohorts was modelled using abundance-at-age survey data by area in the period 2000–2016, covering the region from the northern Bay of Biscay to the eastern Gulf of Cadiz. A novel methodology was used to calculate indices of cohort movement between areas. Movement was relatively low between three large regions, the Bay of Biscay, the northern Spanish and Portuguese waters and the Gulf of Cadiz, each hosting a recruitment hotspot. On the other hand, one half of the sardines recruited in North Portugal and a quarter of those recruited in Southwest Portugal moved to northern Spanish waters and South Portugal, sustaining local populations and fisheries. Movement was mainly driven by recruitment strength and, in a less extent, by food availability during fall. The connectivity and dynamic patterns suggest a metapopulation with three weakly connected populations and density-dependent source-sink movement within the northern Spanish and Portuguese waters population. While the weak connectivity does not invalidate the management boundary between the Bay of Biscay and the Iberian Peninsula, the Gulf of Cadiz may be treated as a separate stock. Multi-area/metapopulation assessment approaches should be applied to account for complex population structure, the higher risks of depleting source areas and/or less productive populations.

Population genomics and climate adaptation of a C4 perennial grass, Panicum hallii (Poaceae)

BackgroundUnderstanding how and why genetic variation is partitioned across geographic space is of fundamental importance to understanding the nature of biological species. How geographical isolation and local adaptation contribute to the formation of ecotypically differentiated groups of plants is just beginning to be understood through population genomic studies. We used whole genome sequencing combined with association study of climate to discover the drivers of differentiation in the perennial C4 grass Panicum hallii.ResultsSequencing of 89 natural accessions of P.hallii revealed complex population structure across the species range. Major population genomic separation was found between subspecies P.hallii var. hallii and var. filipes as well as between at least four major unrecognized subgroups within var. hallii. At least 139 genomic SNPs were significantly associated with temperature or precipitation across the range and these SNPs were enriched for non-synonymous substitutions. SNPs associated with temperature and aridity were more often found in or near genes than expected by chance and enriched for putative involvement in dormancy processes, seed maturation, response to hyperosmosis and salinity, abscisic acid metabolism, hormone metabolism, and drought recovery.ConclusionsBoth geography and climate adaptation contribute significantly to patterns of genome-wide variation in P.hallii. Population subgroups within P.hallii may represent early stages in the formation of ecotypes. Climate associated loci identified here represent promising targets for future research in this and other perennial grasses.

Characteristics of Chernigov’s population by the presentation data

Aim. The population of the world has a complex hierarchical population structure. At the heart of this hierarchy are elementary populations. Methods. Using the quasigenetic marker – surnames – the genetic indices of the population of the Chernihiv region of the rayon and oblast levels were obtained, comparing them with similar indices of the populations of the Poltava (central) and Odessa (borderline) populations. Results. The Chernihiv region is borderline, but the base indicator is an index of isonomy higher (I = 4.57 × 10-4) than in the border region of Odessa, and also more than in the central - Poltava population. The index of inbreeding in the Chernihiv population is Fst = 11.43 × 10-5. The indicator of migration efficiency was v = 17.37 × 10-4 and occupies an intermediate position between the Poltava and Odessa populations. The value of the index H as a whole for the region is 13.24, the index of redundancy of the distribution of names is R = 34.67. Conclusions. The study complements the picture of genetic peculiarity of Ukrainian populations. The genetic characteristics of the Chernihiv population, its difference from the previously studied central Poltava and border area of Odessa, are explained by the peculiarity of the location of the Chernihiv region, the features of the landscape, the other ethnic and civic belonging of the geographically contacting peoples. Keywords: quasigenetic markers, population, isonymy, inbreeding, migration.

High sequence variation in the exon 10 of TSHR gene is associated with flightless-domestic geese.

The genetic and molecular mechanisms of the flightless birds without limb modification are rarely reported. To explore the possible reasons for losing flight ability without limb modification, we used the domestic geese as an ideal model to preliminarily study the possible mechanisms for this kind of flightlessness. We compared the sequence variations of the exon 10 of TSHR gene between three domesticated geese populations and two wild ancestor populations. The results showed that domestic geese had higher genetic diversity and more complex population structure than their wild ancestors. We did not detect any population expansion in domestic geese population. However, we detected clear relaxed selection signal and positive selection in domesticated geese groups. Furthermore, special phylogenetic relationship of the exon 10 of TSHR was observed in domesticated geese groups. Combined with its well-established function on metabolic regulation and photoperiod control, we speculate that relaxed selection of TSHR might have effects on flightlessness of domesticated geese.

Composition of heterotrophic specialized sub-guilds defined by a positive RNA and polyhydroxyalkanoate correlation in activated sludge

Microbial heterotrophic guilds in activated sludge wastewater treatment systems have complex population structures and functions. A previously proposed heterotrophic-specialist model states that heterotrophs consist of sub-guilds specialized in consuming specific classes of compounds, either readily degradable substrate (RDS) or slowly degradable substrate (SDS) according to current mathematical modeling practices for wastewater treatment processes. It follows from metabolic considerations that the levels of RNA and polyhydroxyalkanoate (PHA) are correlated for strains of the same species growing in different environments; a conjecture previously tested. The proposed classification of heterotrophs into RDS or SDS consumers predicts that the same correlation would also be found across heterotrophic species in conventional activated sludge systems; this prediction was tested in the current study. The positive correlation between the RNA and PHA levels was observed in 9 conventional activated sludge plants in two independent sampling times and it was also found stable over a 6-month regular sampling period at one of these plants. Together, these results imply that the levels of RNA and PHA can be used to define heterotrophic-specialist sub-guilds. In order to gain insight in the species composition of the defined sub-guilds, flow cytometry cell sorting was used to further analyze one of the activated sludge samples. Four sorted sub-samples were obtained (high-RNA/high-PHA, low-RNA/high-PHA, high-RNA/low-PHA, and low-RNA/low-PHA), and the phylogenetic composition of each was determined using 16S rRNA gene amplicon pyrosequencing. Heterotrophic genera were identified across 12 phyla, and their representation in each sorted sub-sample showed that the high-RNA/high-PHA and low-RNA/low-PHA groups were most dissimilar. The enriched genera in these sorted sub-samples are suggested to represent the composition of heterotrophic-specialized sub-guilds defined by the kinetics of substrate consumption.

Genotyping-by-sequencing of Brassica oleracea vegetables reveals unique phylogenetic patterns, population structure and domestication footprints

Brassica oleracea forms a diverse and economically significant crop group. Improvement efforts are often hindered by limited knowledge of diversity contained within available germplasm. Here, we employ genotyping-by-sequencing to investigate a diverse panel of 85 landrace and improved B. oleracea broccoli, cauliflower, and Chinese kale entries. Ultimately, 21,680 high-quality SNPs were used to reveal a complex and admixed population structure and clarify phylogenetic relationships among B. oleracea groups. Each broccoli landrace contained, on average, 8.4 times as many unique alleles as an improved broccoli and landraces collectively represented 81% of all broccoli-specific alleles. Commercial broccoli hybrids were largely represented by a single subpopulation identified within a complex population structure. Greater allelic diversity in landrace broccoli and 96.1% of SNPs differentiating improved cauliflower from landrace cauliflower were common to the larger pool of broccoli germplasm, supporting a parallel or later development of cauliflower due to introgression events from broccoli. Chinese kale was readily distinguished by principal coordinate analysis. Genotyping was accomplished with and without reliance upon a reference genome producing 141,317 and 20,815 filtered SNPs, respectively, supporting robust SNP discovery methods in neglected or unimproved crop groups that lack a reference genome. This work clarifies the population structure, phylogeny, and domestication footprints of landrace and improved B. oleracea broccoli using many genotyping-by-sequencing markers. Additionally, a large pool of genetic diversity contained in broccoli landraces is described which may enhance future breeding efforts.

High genetic variability and complex population structure of the native Chinese hazelnut

Corylus mandshurica Maxim. belongs to the family Betulaceae and is an important economically and ecologically tree in China. Wild Corylus mandshurica resources have been gradually destroyed recently. Thus, investigation into the genetic diversity and genetic differentiation is indispensable for the efficient protection and breeding of Corylus mandshurica resources. A total of 347 individuals collected from 12 natural populations were investigated using amplified fragment length polymorphism markers. All 12 Corylus mandshurica populations showed various degrees of genetic diversity, with the value for the Mudanjiang, Heilongjiang Province population reflecting maximum genetic diversity. A UPGMA dendrogram was classified into two main clusters (Cluster I and Cluster II). Moreover, STRUCTURE analysis showed that the result of the divisions at K = 2 was highly related to the UPGMA dendrogram and PCoA scatter plot. The results of both FST and AMOVA suggested that there was low genetic differentiation among different populations. The high level of gene flow among populations can effectively prevent genetic drift. BARRIER analysis indicated that the first barrier boundary located between Cluster I and Cluster II was probably caused by the Yanshan Mountains. Our study provides valuable information for Corylus mandshurica conservation and breeding in the future.

Novel genotypes and multilocus genotypes of Enterocytozoon bieneusi in pigs in northwestern China: A public health concern

Enterocytozoon bieneusi, the most important and common microsporidian species, inhabits in most animals and humans causing diarrhea and systemic diseases. The objectives of the present study were to examine the prevalence and genetic variability of E. bieneusi in pigs in Shaanxi province, northwestern China. A total of 560 pig faecal samples were collected from five different farms in Shaanxi province and molecularly characterized using multilocus genotyping (MLST) technology. High E. bieneusi infection rate (78.9%) was observed in these samples. 12 known and 22 possible novel ITS genotypes were identified, with the novel SZZD1 as the predominant genotype distributed in all age groups and pig farms. 32 (including 11 known and 21 novel ones) of them belong to the zoonotic group 1. MLST analysis showed that 109 ITS positive samples formed 87 distinct multilocus genotypes (MLGs). An incomplete linkage disequilibrium (LD) and clonal genetic structure of E. bieneusi were found in pigs in Shaanxi province. These findings indicated the complex population structures of E. bieneusi in pigs in Shaanxi province and provided baseline data for better understanding of the epidemiological status of E. bieneusi in this province.

Contemporary factors influencing genetic diversity in the Alaska humpback whitefish Coregonus clupeaformis complex.

Thirteen microsatellite loci were used to address three hypotheses regarding genetic diversity in the humpback whitefish Coregonus clupeaformis complex in Alaska. The test results provided further insight into the factors influencing C. clupeaformis complex population structure and level of genetic variation. First, the microsatellite data did not provide evidence of two spatially distinct Beringian and Eurasian refugial groups as revealed in previous phylogeographic analyses of mitochondrial DNA variation. Rather, the population structure inferred from the microsatellite variation appears to reveal the influence of factors on a more recent time scale, including gene flow among the refugial groups and isolation of some anadromous and freshwater resident populations. Second, anadromous C. clupeaformis complex collections exhibited higher intra-population genetic diversity than freshwater resident collections. This outcome is consistent with previous meta analyses suggesting that freshwater resident populations probably have smaller historical effective population sizes and less conspecific gene flow because the habitat tends to be smaller and supports fewer and smaller populations. Finally, the analysis of contemporary immigration rates was consistent with, but did not provide statistical support for, the hypothesis that gene flow among anadromous C. clupeaformis complex populations along coastal Alaska is influenced by the Alaska Coastal Current. Further studies are needed to evaluate gene flow among coastal Alaska C. clupeaformis complex populations.

Genetic factors have a major effect on growth, number of vertebrae and otolith shape in Atlantic herring (Clupea harengus).

Atlantic herring, Clupea harengus, have complex population structures. Mixing of populations is known, but the extent of connectivity is still unclear. Phenotypic plasticity results in divergent phenotypes in response to environmental factors. A marked salinity gradient occurs from Atlantic Ocean (salinity 35) into the Baltic Sea (salinity range 2–12). Herring from both habitats display phenotypic and genetic variability. To explore how genetic factors and salinity influence phenotypic traits like growth, number of vertebrae and otolith shape an experimental population consisting of Atlantic purebreds and Atlantic/Baltic F1 hybrids were incubated and co-reared at two different salinities, 16 and 35, for three years. The F1-generation was repeatedly sampled to evaluate temporal variation. A von Bertalanffy growth model indicated that reared Atlantic purebreds had a higher maximum length (26.2 cm) than Atlantic/Baltic hybrids (24.8 cm) at salinity 35, but not at salinity 16 (25.0 and 24.8 cm, respectively). In contrast, Atlantic/Baltic hybrids achieved larger size-at-age than the wild caught Baltic parental group. Mean vertebral counts and otolith aspect ratios were higher for reared Atlantic purebreds than Atlantic/Baltic hybrids, consistent with the differences between parental groups. There were no significant differences in vertebral counts and otolith aspect ratios between herring with the same genotype but raised in different salinities. A Canonical Analysis of Principal Coordinates was applied to analyze the variation in wavelet coefficients that described otolith shape. The first discriminating axis identified the differences between Atlantic purebreds and Atlantic/Baltic hybrids, while the second axis represented salinity differences. Assigning otoliths based on genetic groups (Atlantic purebreds vs. Atlantic/Baltic hybrids) yielded higher classification success (~90%) than based on salinities (16 vs. 35; ~60%). Our results demonstrate that otolith shape and vertebral counts have a significant genetic component and are therefore useful for studies on population dynamics and connectivity.

The origins of diversity in ancient landscapes: Deep phylogeographic structuring in a pseudoscorpion (Pseudotyrannochthoniidae: Pseudotyrannochthonius) reflects Plio-Pleistocene climate fluctuations

Southwestern Australia is one of the global biodiversity hotspots. Like many other hotspots, comparatively few data are available explaining speciation patterns in endemic animal lineages, which hampers conservation efforts and a deeper understanding of how diversity is generated and maintained. I investigated the phylogeographic structure of an ancient arachnid species, the pseudoscorpion Pseudotyrannochthonius giganteus Beier, 1971, endemic to the mesic eucalypt forests of southwestern Australia. This species is habitat-restricted and has morphologically divergent populations in epigean (forest) and hypogean (karst) habitats. Phylogenetic, molecular clock and population genetic analyses of mitochondrial (COI mtDNA) and nuclear (ITS2 rDNA) data revealed a complex population structure, with six allopatric lineages separated by vicariant barriers, such as rivers. These lineages diverged between the late Miocene and Pliocene epochs, characterised by increasingly intense climatic cycles between mesic/warm and arid/cold. Surprisingly, specimens from caves were genetically similar to those from forests, indicating subterranean isolation has not driven diversification. Instead, genetic diversity is clustered in a small area, coinciding with the highest rainfall and lowest seasonality in Western Australia. Future climates, warmer and drier than today, will likely lead to range retraction towards this area and mimic past variations that have shaped contemporary diversity. Southwestern Australia is an ancient, stable landscape that allowed for persistence of ancient lineages, such as P. giganteus. Historic climatic fluctuations have driven diversification, generating highly structured species and localised centres of endemism. Other ancient landscapes, e.g. South Africa’s Cape Provinces, are expected to share similarly complex patterns of invertebrate biodiversity. Unravelling these is essential to informed conservation decision making.