The evolution of sexual and parthenogenetic Warramaba: a window onto Plio-Pleistocene diversification processes in an arid biome

True Parthenogenesis and Female-Biased Sex Ratios in Cicadomorpha and Fulgoromorpha (Hemiptera, Auchenorrhyncha)

Insects are renowned for their remarkable diversity of reproductive modes. Among these, the largest non-holometabolous order, Hemiptera, stands out with one of the most diversified arrays of parthenogenesis modes observed among insects. Although there are extensive reviews on reproduction without fertilization in some hemipteran higher taxa, no such analysis has been conducted for the large suborders Fulgoromorpha (planthoppers) and Cicadomorpha (leafhoppers). In both groups, there are species that reproduce by true parthenogenesis, specifically thelytoky, and in Fulgoromorpha, there are species that reproduce by pseudogamy or, more specifically, sperm-dependent parthenogenesis. In this review paper, we give and discuss the only currently known examples of true parthenogenesis in Fulgoromorpha and Cicadomorpha, mainly from the planthopper family Delphacidae and the leafhopper family Cicadellidae. We analyze patterns of distribution, ecology, mating behavior, acoustic communication, and cytogenetic and genetic diversity of parthenoforms and discuss hypotheses about the origin of parthenogenesis in each case. We also highlight examples in which natural populations show a shift in sex ratio toward females and discuss possible causes of this phenomenon, primarily the influence of endosymbiotic bacteria capable of altering the reproductive strategies of the hosts. Our review is mainly based on studies in which the authors have participated.

Parthenogenesis without costs in a grasshopper with hybrid origins

The rarity of parthenogenetic species is typically attributed to the reduced genetic variability that accompanies the absence of sex, yet natural parthenogens can be surprisingly successful. Ecological success is often proposed to derive from hybridization through enhanced genetic diversity from repetitive origins or enhanced phenotypic breadth from heterosis. Here, we tested and rejected both hypotheses in a classic parthenogen, the diploid grasshopper Warramaba virgo. Genetic data revealed a single hybrid mating origin at least 0.25 million years ago, and comparative analyses of 14 physiological and life history traits showed no evidence for altered fitness relative to its sexual progenitors. Our findings imply that the rarity of parthenogenesis is due to constraints on origin rather than to rapid extinction.

Revision of a unique Australian leafhopper genus Stenopsoides Evans (Hemiptera: Cicadellidae: Idiocerinae: Macropsini)

The Australian genus Stenopsoides Evans (Idiocerinae: Macropsini) is revised. The type species, S. turneri Evans, is redescribed and three new species are added: S. newi Semeraro sp. nov., S. punctatus Semeraro sp. nov. and S. truncatus Semeraro sp. nov.. Species photographic plates, a distribution map and an illustrated key to the four species are provided. The possibility of parthenogenetic reproduction occuring in this genus is discussed.

Origin, clonal diversity, and evolution of the parthenogenetic lizard Darevskia unisexualis

BACKGROUND

The hybridization of female D. raddei and male D. valentini gave rise to the parthenogenetic Caucasian rock lizard Darevskia unisexualis. A previously identified genetic polymorphism in the species consisted of one common and two allozyme clones. Analysis of microsatellites and single nucleotide polymorphisms (SNPs) from the three species yields estimates of clonal diversity and tests the hypothesis of a single origin for D. unisexualis.

RESULTS

Genotyping and sequencing of four microsatellite-containing loci for 109 specimens of D. unisexualis, 17 D. valentini, and 45 D. raddei nairensis identified 12 presumptive clones, including one widespread and 11 rare clones. Most individuals in some localities had a rare clone. Clone-specific alleles in D. unisexualis were compared with those of the parental species. The results inferred a single hybridization event. Post-formation mutations best explain the less common clones.

CONCLUSIONS

Interspecific analyses identify alleles inherited by D. unisexualis from its bisexual ancestors. SNP analyses fail to reject the hypothesis of a single interspecific origin of D. unisexualis, followed by microsatellite mutations in this initial clone. Microsatellites detect higher clonal diversity in D. unisexualis compared to allozymes and identify the likely origins of clones. Our approach may be applicable to other unisexual species whose origins involve interspecific hybridization.

Isolation and Lack of Potential Mates may Threaten an Endangered Arid-Zone Acacia

Clonality may provide reproductive assurance for many threatened plants while limiting sexual reproductive success either through energetic tradeoffs or because clones are self-incompatible. Most stands of the Australian arid-zone plant Acacia carneorum, flower annually but low seed set and an absence of sexual recruitment now suggest that this species and other, important arid-zone ecosystem engineers may have low genotypic diversity. Indeed, our recent landscape-scale genetic study revealed that stands are typically monoclonal, with genets usually separated by kilometers. An inability to set sexually produced seed or a lack of genetically diverse mates may explain almost system-wide reproductive failure. Here, using microsatellite markers, we genotyped 100 seeds from a rare fruiting stand (Middle-Camp), together with all adult plants within it and its 4 neighboring stands (up to 5 km distant). As expected, all stands surveyed were monoclonal. However, the Middle-Camp seeds were generated sexually. Comparing seed genotypes with the single Middle-Camp genotype and those of genets from neighboring and other regional stands (n = 26), revealed that 73 seeds were sired by the Middle-Camp genet. Within these Middle-Camp seeds we detected 19 genotypes in proportions consistent with self-fertilization of that genet. For the remaining 27 seeds, comprising 8 different genotypes, paternity was assigned to the nearest neighboring stands Mallee and Mallee-West, approximately 1 km distant. Ironically, given this species' vast geographic range, a small number of stands with reproductively compatible near neighbors may provide the only sources of novel genotypes.

Linking thermal adaptation and life-history theory explains latitudinal patterns of voltinism

Insect life cycles are adapted to a seasonal climate by expressing alternative voltinism phenotypes-the number of generations in a year. Variation in voltinism phenotypes along latitudinal gradients may be generated by developmental traits at critical life stages, such as eggs. Both voltinism and egg development are thermally determined traits, yet independently derived models of voltinism and thermal adaptation refer to the evolution of dormancy and thermal sensitivity of development rate, respectively, as independent influences on life history. To reconcile these models and test their respective predictions, we characterized patterns of voltinism and thermal response of egg development rate along a latitudinal temperature gradient using the matchstick grasshopper genus Warramaba. We found remarkably strong variation in voltinism patterns, as well as corresponding egg dormancy patterns and thermal responses of egg development. Our results show that the switch in voltinism along the latitudinal gradient was explained by the combined predictions of the evolution of voltinism and of thermal adaptation. We suggest that latitudinal patterns in thermal responses and corresponding life histories need to consider the evolution of thermal response curves within the context of seasonal temperature cycles rather than based solely on optimality and trade-offs in performance. This article is part of the theme issue 'Physiological diversity, biodiversity patterns and global climate change: testing key hypotheses involving temperature and oxygen'.

Recent range expansion in Australian hummock grasses (Triodia) inferred using genotyping-by-sequencing

The Australian arid zone (AAZ) has undergone aridification and the formation of vast sandy deserts since the mid-Miocene. Studies on AAZ organisms, particularly animals, have shown patterns of mesic ancestry, persistence in rocky refugia and range expansions in arid lineages. There has been limited molecular investigation of plants in the AAZ, particularly of taxa that arrived in Australia after the onset of aridification. Here we investigate populations of the widespread AAZ grass Triodia basedowii to determine whether there is evidence for a recent range expansion, and if so, its source and direction. We also undertake a dating analysis for the species complex to which T. basedowii belongs, in order to place its diversification in relation to changes in AAZ climate and landscapes. We analyse a genomic single nucleotide polymorphism data set from 17 populations of T. basedowii in a recently developed approach for detecting the signal and likely origin of a range expansion. We also use alignments from existing and newly sequenced plastomes from across Poaceae for analysis in BEAST to construct fossil-calibrated phylogenies. Across a range of sampling parameters and outgroups, we detected a consistent signal of westward expansion for T. basedowii, originating in central or eastern Australia. Divergence time estimation indicates that Triodia began to diversify in the late Miocene (crown 7.0-8.8 million years (Ma)), and the T. basedowii complex began to radiate during the Pleistocene (crown 1.4-2.0 Ma). This evidence for range expansion in an arid-adapted plant is consistent with similar patterns in AAZ animals and likely reflects a general response to the opening of new habitat during aridification. Radiation of the T. basedowii complex through the Pleistocene has been associated with preferences for different substrates, providing an explanation why only one lineage is widespread across sandy deserts.

Clonality disguises the vulnerability of a threatened arid zone Acacia

Long-lived, widespread plant species are expected to be genetically diverse, reflecting the interaction between large population sizes, overlapping generations, and gene flow. Such species are thought to be resilient to disturbance, but may carry an extinction debt due to reproductive failure. Genetic studies of Australian arid zone plant species suggest an unusually high frequency of asexuality, polyploidy, or both. A preliminary AFLP genetic study implied that the naturally fragmented arid zone tree, Acacia carneorum, is almost entirely dependent on asexual reproduction through suckering, and stands may have lacked genetic diversity and interconnection even prior to the onset of European pastoralism. Here we surveyed microsatellite genetic variation in 20 stands to test for variation in life histories and further assessed the conservation status of the species by comparing genetic diversity within protected stands in National Parks and disturbed range lands. Using herbarium records, we estimate that 219 stands are extant, all of which occur in the arid zone, west of the Darling River in southeastern Australia. With two exceptions, all surveyed stands comprised only one multilocus genet and at least eight were putatively polyploid. Although some stands comprise thousands of stems, our findings imply that the species as a whole may represent ~240 distinct genetic individuals, many of which are polyploid, and most are separated by >10 km of unsuitable habitat. With only 34% of stands (and therefore genets) occurring within conservation reserves, A. carneorum may be at much greater risk of extinction than inferred from on-ground census data. Land managers should prioritize on-ground preservation of the genotypes within existing reserves, protecting both vegetative suckers and seedlings from herbivory. Importantly, three stands are known to set viable seed and should be used to generate genetically diverse germ-plasm for ex situ conservation, population augmentation, or translocation.

The origin of multiple clones in the parthenogenetic lizard species Darevskia rostombekowi

The all-female Caucasian rock lizard Darevskia rostombekowi and other unisexual species of this genus reproduce normally via true parthenogenesis. Typically, diploid parthenogenetic reptiles exhibit some amount of clonal diversity. However, allozyme data from D. rostombekowi have suggested that this species consists of a single clone. Herein, we test this hypothesis by evaluating variation at three variable microsatellite loci for 42 specimens of D. rostombekowi from four populations in Armenia. Analyses based on single nucleotide polymorphisms of each locus reveal five genotypes or presumptive clones in this species. All individuals are heterozygous at the loci. The major clone occurs in 24 individuals and involves three populations. Four rare clones involve one or several individuals from one or two populations. Most variation owes to parent-specific single nucleotide polymorphisms, which occur as heterozygotes. This result fails to reject the hypothesis of a single hybridization founder event that resulted in the initial formation of one major clone. The other clones appear to have originated via post-formation microsatellite mutations of the major clone.

Rapid and recent diversification patterns in Anseriformes birds: Inferred from molecular phylogeny and diversification analyses

The Anseriformes is a well-known and widely distributed bird order, with more than 150 species in the world. This paper aims to revise the classification, determine the phylogenetic relationships and diversification patterns in Anseriformes by exploring the Cyt b, ND2, COI genes and the complete mitochondrial genomes (mito-genomes). Molecular phylogeny and genetic distance analyses suggest that the Dendrocygna species should be considered as an independent family, Dendrocygnidae, rather than a member of Anatidae. Molecular timescale analyses suggests that the ancestral diversification occurred during the Early Eocene Climatic Optimum (58 ~ 50 Ma). Furthermore, diversification analyses showed that, after a long period of constant diversification, the median initial speciation rate was accelerated three times, and finally increased to approximately 0.3 sp/My. In the present study, both molecular phylogeny and diversification analyses results support that Anseriformes birds underwent rapid and recent diversification in their evolutionary history, especially in modern ducks, which show extreme diversification during the Plio-Pleistocene (~ 5.3 Ma). Therefore, our study support that the Plio-Pleistocene climate fluctuations are likely to have played a significant role in promoting the recent diversification for Anseriformes.

Extreme genetic diversity in asexual grass thrips populations

The continuous generation of genetic variation has been proposed as one of the main factors explaining the maintenance of sexual reproduction in nature. However, populations of asexual individuals may attain high levels of genetic diversity through within-lineage diversification, replicate transitions to asexuality from sexual ancestors and migration. How these mechanisms affect genetic variation in populations of closely related sexual and asexual taxa can therefore provide insights into the role of genetic diversity for the maintenance of sexual reproduction. Here, we evaluate patterns of intra- and interpopulation genetic diversity in sexual and asexual populations of Aptinothrips rufus grass thrips. Asexual A. rufus populations are found throughout the world, whereas sexual populations appear to be confined to few locations in the Mediterranean region. We found that asexual A. rufus populations are characterized by extremely high levels of genetic diversity, both in comparison with their sexual relatives and in comparison with other asexual species. Migration is extensive among asexual populations over large geographic distances, whereas close sexual populations are strongly isolated from each other. The combination of extensive migration with replicate evolution of asexual lineages, and a past demographic expansion in at least one of them, generated high local clone diversities in A. rufus. These high clone diversities in asexual populations may mimic certain benefits conferred by sex via genetic diversity and could help explain the extreme success of asexual A. rufus populations.

Do clones degenerate over time? Explaining the genetic variability of asexuals through population genetic models

Background

Quest for understanding the nature of mechanisms governing the life span of clonal organisms lasts for several decades. Phylogenetic evidence for recent origins of most clones is usually interpreted as proof that clones suffer from gradual age-dependent fitness decay (e.g. Muller's ratchet). However, we have shown that a neutral drift can also qualitatively explain the observed distribution of clonal ages. This finding was followed by several attempts to distinguish the effects of neutral and non-neutral processes. Most recently, Neiman et al. 2009 (Ann N Y Acad Sci.:1168:185-200.) reviewed the distribution of asexual lineage ages estimated from a diverse array of taxa and concluded that neutral processes alone may not explain the observed data. Moreover, the authors inferred that similar types of mechanisms determine maximum asexual lineage ages in all asexual taxa. In this paper we review recent methods for distinguishing the effects of neutral and non-neutral processes and point at methodological problems related with them.

Results and Discussion

We found that contemporary analyses based on phylogenetic data are inadequate to provide any clear-cut answer about the nature and generality of processes affecting evolution of clones. As an alternative approach, we demonstrate that sequence variability in asexual populations is suitable to detect age-dependent selection against clonal lineages. We found that asexual taxa with relatively old clonal lineages are characterised by progressively stronger deviations from neutrality.

Conclusions

Our results demonstrate that some type of age-dependent selection against clones is generally operational in asexual animals, which cover a wide taxonomic range spanning from flatworms to vertebrates. However, we also found a notable difference between the data distribution predicted by available models of sequence evolution and those observed in empirical data. These findings point at the possibility that processes affecting clonal evolution differ from those described in recent studies, suggesting that theoretical models of asexual populations must evolve to address this problem in detail.

Reviewers

This article was reviewed by Isa Schön (nominated by John Logsdon), Arcady Mushegian and Timothy G. Barraclough (nominated by Laurence Hurst).

Nuclear gene phylogeography using PHASE: dealing with unresolved genotypes, lost alleles, and systematic bias in parameter estimation

Background

A widely-used approach for screening nuclear DNA markers is to obtain sequence data and use bioinformatic algorithms to estimate which two alleles are present in heterozygous individuals. It is common practice to omit unresolved genotypes from downstream analyses, but the implications of this have not been investigated. We evaluated the haplotype reconstruction method implemented by PHASE in the context of phylogeographic applications. Empirical sequence datasets from five non-coding nuclear loci with gametic phase ascribed by molecular approaches were coupled with simulated datasets to investigate three key issues: (1) haplotype reconstruction error rates and the nature of inference errors, (2) dataset features and genotypic configurations that drive haplotype reconstruction uncertainty, and (3) impacts of omitting unresolved genotypes on levels of observed phylogenetic diversity and the accuracy of downstream phylogeographic analyses.

Results

We found that PHASE usually had very low false-positives (i.e., a low rate of confidently inferring haplotype pairs that were incorrect). The majority of genotypes that could not be resolved with high confidence included an allele occurring only once in a dataset, and genotypic configurations involving two low-frequency alleles were disproportionately represented in the pool of unresolved genotypes. The standard practice of omitting unresolved genotypes from downstream analyses can lead to considerable reductions in overall phylogenetic diversity that is skewed towards the loss of alleles with larger-than-average pairwise sequence divergences, and in turn, this causes systematic bias in estimates of important population genetic parameters.

Conclusions

A combination of experimental and computational approaches for resolving phase of segregating sites in phylogeographic applications is essential. We outline practical approaches to mitigating potential impacts of computational haplotype reconstruction on phylogeographic inferences. With targeted application of laboratory procedures that enable unambiguous phase determination via physical isolation of alleles from diploid PCR products, relatively little investment of time and effort is needed to overcome the observed biases.

Inference of population history by coupling exploratory and model-driven phylogeographic analyses

Understanding the nature, timing and geographic context of historical events and population processes that shaped the spatial distribution of genetic diversity is critical for addressing questions relating to speciation, selection, and applied conservation management. Cladistic analysis of gene trees has been central to phylogeography, but when coupled with approaches that make use of different components of the information carried by DNA sequences and their frequencies, the strength and resolution of these inferences can be improved. However, assessing concordance of inferences drawn using different analytical methods or genetic datasets, and integrating their outcomes, can be challenging. Here we overview the strengths and limitations of different types of genetic data, analysis methods, and approaches to historical inference. We then turn our attention to the potentially synergistic interactions among widely-used and emerging phylogeographic analyses, and discuss some of the ways that spatial and temporal concordance among inferences can be assessed. We close this review with a brief summary and outlook on future research directions.

Diversification and persistence at the arid-monsoonal interface: australia-wide biogeography of the Bynoe's gecko (Heteronotia binoei; Gekkonidae)

Late Neogene aridification in the Southern Hemisphere caused contractions of mesic biota to refugia, similar to the patterns established by glaciation in the Northern Hemisphere, but these episodes also opened up new adaptive zones that spurred range expansion and diversification in arid-adapted lineages. To understand these dynamics, we present a multilocus (nine nuclear introns, one mitochondrial gene) phylogeographic analysis of the Bynoe's gecko (Heteronotia binoei), a widely distributed complex spanning the tropical monsoon, coastal woodland, and arid zone biomes in Australia. Bayesian phylogenetic analyses, estimates of divergence times, and demographic inferences revealed episodes of diversification in the Pliocene, especially in the tropical monsoon biome, and range expansions in the Pleistocene. Ancestral habitat reconstructions strongly support recent and independent invasions into the arid zone. Our study demonstrates the varied responses to aridification in Australia, including localized persistence of lineages in the tropical monsoonal biome, and repeated invasion of and expansion through newly available arid-zone habitats. These patterns are consistent with those found in other arid environments in the Southern Hemisphere, including the South African succulent karoo and the Chilean lowlands, and highlight the diverse modes of diversification and persistence of Earth's biota during the glacial cycles of the Pliocene and Pleistocene.