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opencc-zeroDec 2012View details →

Data from: Home loving boreal hare mitochondria survived several invasions in Iberia: the relative roles of recurrent hybridisation and allele surfing

Genetic introgression from a resident species into an invading close relative can result from repeated hybridisation along the invasion front and/or allele surfing on the expansion wave. Cases where the phenomenon is massive and systematic, such as for hares (genus Lepus) in Iberia, would be best explained by recurrent hybridisation but this is difficult to prove since the donor populations are generally extinct. In the Pyrenean foothills, Lepus europaeus presumably replaced Lepus granatensis recently and the present species border is parallel to the direction of invasion, so that populations of L. granatensis in the contact zone represent proxies of existing variation before the invasion. Among three pairs of populations sampled across this border, we find less differentiation of mtDNA across than along it, as predicted under recurrent hybridisation at the invasion front. Using autosomal microsatellite loci and X and Y-linked diagnostic loci, we show that admixture across the border is quasi-absent, making it unlikely that lack of interspecific mtDNA differentiation result from ongoing gene flow. Furthermore, we find that the local species ranges are climatically contrasted, making it also unlikely that ongoing ecology-driven movement of the contact account for mtDNA introgression. The lack of mtDNA differentiation across the boundary is mostly due to sharing of mtDNA from a boreal species currently extinct in Iberia (Lepus timidus) whose mitochondria have thus remained in place since the last deglaciation despite successive invasions by two other species. Home loving mitochondria thus witness past species distribution rather than ongoing exchanges across stabilised contact zones.

opencc-zeroDec 2016View details →

Data from: Maintaining their genetic distance: little evidence for introgression between widely hybridising species of Geum with contrasting mating systems

Within the plant kingdom many genera contain sister lineages with contrasting outcrossing and inbreeding mating systems that are known to hybridise. The evolutionary fate of these sister lineages is likely to be influenced by the extent to which they exchange genes. We measured gene flow between outcrossing Geum rivale and selfing G. urbanum, sister species that hybridise in contemporary populations. We generated and used a draft genome of G. urbanum to develop dd-RAD data scorable in both species. Coalescent analysis of RAD data from allopatric populations indicated that the species diverged 2-3 Mya, and that historical gene flow between them was extremely low (1 migrant every 25 generations). Comparison of genetic divergence between species in sympatry and allopatry, together with an analysis of allele frequencies in potential parental and hybrid populations, provided no evidence of contemporary introgression in sympatric populations. Cluster and species specific marker analyses revealed that, apart from four early generation hybrids, individuals in sympatric populations fell into two genetically distinct groups that corresponded exactly to their morphological species classification with maximum individual admixture estimates of only 1 -3%. However, we did observe joint segregation of four putatively introgressed SNPs across two scaffolds in the G. urbanum population that was associated with significant morphological variation, interpreted as tentative evidence for rare, recent interspecific gene flow. Overall, our results indicate that despite the presence of hybrids in contemporary populations, genetic exchange between G. rivale and G. urbanum has been extremely limited throughout their evolutionary history.

opencc-zeroDec 2017View details →

Data from: Recurrent hybridisation events between Primula vulgaris, P. veris and P. elatior (Primulaceae, Ericales) challenge the species boundaries: Using molecular markers to re‐evaluate morphological identifications

Three Primula species, Primula vulgaris, P. veris and P. elatior, have been objects of fascination for gardeners and botanists over several centuries. The species are able to hybridise, and where they co-occur, hybrids are commonly found. In Denmark, Møns Klint on the island of Møn and Købelev Skov on Lolland are examples of localities where all three species occur and where the hybrids P. ×digenea, the hybrid between P. vulgaris and P. elatior, and P. ×polyantha, the hybrid between P. veris and P. vulgaris, can also be found. To investigate relations between the species and their hybrids, 168 specimens from 10 geographical locations were sampled for genetic analysis using DNA markers and identified based on morphological traits, primarily inflorescense structure, the size, shape, colour and markings of corolla and leaf basis, leaf blade texture and hairiness. After identifying species-specific SNPs in the internal transcribed spacer sequence, these were used to resolve species and hybrid boundaries and status through a cleaved amplified polymorphic sequence assay. Polymorphisms in the chloroplast trnL sequence were used as a high-throughput marker and used to determine the maternal parent of hybrids. Ten simple sequence repeat markers were applied to obtain further insight into the genetic makeup of the accessions using Structure and Introgress, providing information of genetic variability within and between populations. Data analyses indicated that backcrossing of P. ×digenea hybrids with parental species has occurred, and that many of the P. ×digenea found in the study were later-generation hybrids rather than F1s. Analyses of P. ×polyantha specimens show mostly the expected pattern for primary hybrids but indications of P. veris ancestry of a P. vulgaris plant was discovered. Our results further indicate that some of the specimens initially identified as P. elatior include P. vulgaris among their progenitors and thus challenge currently accepted species boundaries.

opencc-zeroDec 2021View details →

Hybridisation boosts dispersal of two contrasted ecotypes in a grass species

Genetic exchanges between closely related groups of organisms with different adaptations have well-documented beneficial and detrimental consequences. In plants, pollen-mediated exchanges affect the sorting of alleles across physical landscapes, and influence rates of hybridisation. How these dynamics affect the emergence and spread of novel ecological strategies remains only partially understood. Here, we use phylogenomics and population genomics to retrace the origin and spread of two geographically overlapping ecotypes of the African grass Alloteropsis angusta. Besides an ecotype inhabiting wetlands, we report the existence of a previously undescribed ecotype inhabiting miombo woodlands and grasslands. The two ecotypes are consistently associated with different nuclear groups, which represent an advanced stage of divergence with secondary low-level gene flow. However, the seed-transported chloroplast genomes are consistently shared by distinct ecotypes inhabiting the same region. These patterns suggest that the nuclear genome of one ecotype can reach the seeds of the other via occasional pollen movements with sorting of nuclear groups in subsequent generations. The contrasting ecotypes of A. angusta can thus use each other as a gateway to new locations across a large part of Africa, showing that hybridisation can facilitate the geographical dispersal of distinct ecotypes of the same grass species.

opencc-zeroAug 2022View details →

Hybridisation and chloroplast capture between distinct Themeda triandra lineages in Australia

Ecotypes are distinct populations within a species that are adapted to specific environmental conditions. Understanding how these ecotypes become established, and how they interact when reunited, is fundamental to elucidating how ecological adaptations are maintained. This study focuses on Themeda triandra, a dominant grassland species across Asia, Africa and Australia. It is the most widespread plant in Australia, where it has distinct ecotypes that are usually restricted to either wetter and cooler coastal regions or the drier and hotter interior. We generate a de novo reference genome for T. triandra and use whole genome sequencing for over 80 Themeda accessions to reconstruct the evolutionary history of T. triandra and related taxa. Organelle phylogenies confirm that Australia was colonised by T. triandra twice, with the division between ecotypes predating their arrival in Australia. The nuclear genome provides evidence of differences in the dominant ploidal level and gene-flow among the ecotypes. In northern Queensland there appears to be a hybrid zone between ecotypes with admixed nuclear genomes and shared chloroplast haplotypes. Conversely, in the cracking claypans of Western Australia, there is cytonuclear discordance with individuals possessing the coastal chloroplast and interior clade nuclear genome. This chloroplast capture is potentially a result of adaptive introgression, with selection detected in the rpoC2 gene which is associated with water use efficiency. The reason why T. triandra is the most widespread plant in Australia appears to be a result of distinct ecotypic genetic variation and genome duplication, with the importance of each depending on the geographic scale considered.

opennotspecifiedMar 2019View details →

Fig. 2 in COI-based species delimitation in Indochinese Tetraserica chafers reveal hybridisation despite strong divergence in male copulation organs

Fig. 2 Tree from Bayesian inference along with the information about morphospecies assignment (column morphology, paraphyletic morphospecies red), collecting sites (cf. Fig. 1), results from the various methods of species delimitation (columns 3–8, mPTP and GMYC with results for all specimens (all) and for unique haplotypes (ht)) and illustrations of the respective morphospecies' aedeagi. Green boxes indicate

opennotspecifiedMar 2019View details →

Fig. 1 in COI-based species delimitation in Indochinese Tetraserica chafers reveal hybridisation despite strong divergence in male copulation organs

Fig. 1 Map of Southeast Asia showing collecting sites of studied individuals. Numbers refer to Supplement Table 1 and Fig. 2

opencc-zeroDec 2011View details →

Data from: Hybridisation and genetic diversity in introduced Mimulus (Phrymaceae)

Hybridisation among taxa with different ploidy levels is often associated with hybrid sterility. Clonal reproduction can stabilise these hybrids, but pervasive clonality may have a profound impact on the distribution of genetic diversity in natural populations. Here we investigate a widespread triploid taxon resulting from hybridisation between diploid Mimulus guttatus and tetraploid Mimulus luteus, two species that were introduced into the United Kingdom (UK) in the nineteenth century. This hybrid, Mimulus x robertsii, is largely sterile but capable of prolific vegetative propagation and has been recorded in the wild since 1872. We surveyed 40 Mimulus populations from localities across the UK to examine the current incidence of hybrids, and selected seventeen populations for genetic analysis using codominant markers. Cluster analyses revealed two main groups of genetically distinct individuals, corresponding to either diploid (M. guttatus) or polyploid (M. luteus and M. x robertsii) samples. Triploid hybrids were found in around 50% of sampled sites, sometimes coexisting with one of the parental species (M. guttatus). The other parent, M. luteus, was restricted to a single locality. Individual populations of M. x robertsii were genetically variable, containing multiple, highly heterozygous clones, with the majority of genetic variation distributed among- rather than within populations. Our findings demonstrate that this largely sterile, clonal taxon can preserve non-negligible amounts of genetic variation. The presence of genetically variable hybrid populations may provide the material for the continued success of asexual taxa in diverse environments.

FIGURE 59 in A revision of the Pauropsalta annulata Goding & Froggatt species group (Hemiptera: Cicadidae) based on morphology, calling songs and ecology, with investigations into calling song structure, molecular phylogenetic relationships and a case of hybridisation between two subspecies

FIGURE 59. Chronogram showing an estimated phylogeny with divergence times for the Pauropsalta annulata species group, along with outgroups from the tribe Cicadettini, based on CO1 and dynamin data (modelled independently). The topology is a maximum clade credibility from an MCMC search, enforcing a relaxed molecular clock with branch lengths modelled using a GTR + I + G model in *BEAST. Node support is indicated by black closed circles (BPP=1.00) and grey closed circles (BPP=0.95–0.99) from BEAST. Clock calibration is based on a rate of 0.0115s/s/myr for CO1 (see Phylogenetic Analysis Methodology section).

FIGURE 55 in A revision of the Pauropsalta annulata Goding & Froggatt species group (Hemiptera: Cicadidae) based on morphology, calling songs and ecology, with investigations into calling song structure, molecular phylogenetic relationships and a case of hybridisation between two subspecies

FIGURE 55. Results of two Non-metric Multidimensional Scaling ordination analyses using the durations of the four song segments (Fig. 54) for Pauropsalta annulata (red), Pauropsalta tremula (purple), Pauropsalta notialis notialis (orange), Pauropsalta notialis incitata (blue) and Pauropsalta notialis notialisxincitata (green) (n=532). Closed points denote individuals recorded in sympatry with other species in the P. annulata species complex, whereas open outlined points are individuals recorded in allopatry. A cluster analysis revealed five clusters among the data, as indicated, and the composition of each is detailed in the text.

FIGURE 52 in A revision of the Pauropsalta annulata Goding & Froggatt species group (Hemiptera: Cicadidae) based on morphology, calling songs and ecology, with investigations into calling song structure, molecular phylogenetic relationships and a case of hybridisation between two subspecies

FIGURE 52. Male calling song structure of Pauropsalta ayrensis Ewart illustrated in expanded waveform plots (explained in Fig. 8), showing both buzzing and lilting components. The spectrogram at the bottom of the figure displays song frequency, which exhibits no modulation between the song components in this species. This specimen was recorded in the field at Eidsvold (25°22'S 151°07'E).

FIGURE 51 in A revision of the Pauropsalta annulata Goding & Froggatt species group (Hemiptera: Cicadidae) based on morphology, calling songs and ecology, with investigations into calling song structure, molecular phylogenetic relationships and a case of hybridisation between two subspecies

FIGURE 51. Map of eastern Australia showing the geographical distribution of Pauropsalta ayrensis Ewart. Large triangles represent specimen records (see material examined) and small triangles represent aural records (some recorded).

FIGURE 50 in A revision of the Pauropsalta annulata Goding & Froggatt species group (Hemiptera: Cicadidae) based on morphology, calling songs and ecology, with investigations into calling song structure, molecular phylogenetic relationships and a case of hybridisation between two subspecies

FIGURE 50. Waveform plots illustrating the lilting component of the male calling song of Pauropsalta rubristrigata (Goding and Froggatt) from four different localities, including: (i) Penola (37°24'S 140°50'E), (ii) Nimmitabel (36°31'S 149°14'E), (iii) Napoleon Reef (33°26'S149°45'E), and (iv) Woods Reserve (35°28'S 148°57'E). Recording (iv) is shown in two fragments from the same individual recording. Mean phrase repetition rates (PRR) for each recording are provided to the right of each plot for reference. The upper fragment shows the typical lilting component and the lower fragment illustrates a transition into the extended lilting component (a grey dashed line indicates the point of transition). Recording (i) was made with RS6 by B. Haywood, while all other recordings were made by LWP using RS5 (see methods).

FIGURE 49 in A revision of the Pauropsalta annulata Goding & Froggatt species group (Hemiptera: Cicadidae) based on morphology, calling songs and ecology, with investigations into calling song structure, molecular phylogenetic relationships and a case of hybridisation between two subspecies

FIGURE 49. Male calling song structure of Pauropsalta rubristrigata (Goding and Froggatt) illustrated in expanded waveform plots (explained in Fig. 8), showing both buzzing and lilting components. The spectrogram at the bottom of the figure displays song frequency, which exhibits no modulation between the song components in this species. This specimen was recorded in the field at Nimmitabel (36°31'S 149°14'E) using RS5 (see methods).

FIGURE 56 in A revision of the Pauropsalta annulata Goding & Froggatt species group (Hemiptera: Cicadidae) based on morphology, calling songs and ecology, with investigations into calling song structure, molecular phylogenetic relationships and a case of hybridisation between two subspecies

FIGURE 56. Phylogram showing an estimated phylogeny for the Pauropsalta annulata species group, along with outgroups from the tribe Cicadettini, based on CO1 data. The topology is a majority rule consensus tree from an MCMC search, with branch lengths simulated using a GTR + I + G model in MrBayes. Node support values to the left of each node are from a RAxML reconstruction, with Bayesian Posterior Probabilities (BPP) from MrBayes represented by small closed circles (BPP=0.95–0.99) and large closed circles (BPP=1.00) on the relevant nodes.

FIGURE 54 in A revision of the Pauropsalta annulata Goding & Froggatt species group (Hemiptera: Cicadidae) based on morphology, calling songs and ecology, with investigations into calling song structure, molecular phylogenetic relationships and a case of hybridisation between two subspecies

FIGURE 54. Oscillogram showing two phrases from the lilting part of the male calling song of Pauropsalta notialis incitata. This is the component to which the female responds during acoustic duets, as shown on the figure. The durations of the various song segments that are demarcated with lines were measured for statistical comparisons, including the long echeme (segment 1), silence between echemes (segment 2), short echeme (segment 3) and silence for female response (segment 4).

FIGURE 47 in A revision of the Pauropsalta annulata Goding & Froggatt species group (Hemiptera: Cicadidae) based on morphology, calling songs and ecology, with investigations into calling song structure, molecular phylogenetic relationships and a case of hybridisation between two subspecies

FIGURE 47. Male calling song structure of Pauropsalta inversa sp. nov. illustrated in expanded waveform plots (explained in Fig. 8), showing both buzzing and lilting components. The spectrogram at the bottom of the figure displays song frequency, which exhibits no modulation between the song components in this species. This specimen was recorded in the field at Eidsvold (25°22'S 151°07'E).

FIGURE 45 in A revision of the Pauropsalta annulata Goding & Froggatt species group (Hemiptera: Cicadidae) based on morphology, calling songs and ecology, with investigations into calling song structure, molecular phylogenetic relationships and a case of hybridisation between two subspecies

FIGURE 45. Waveform plots illustrating the male calling song of Pauropsalta corymbiae sp. nov. from six different localities, including: (i) Bull's Gully via Adavale (25°58'S 144°59'E), (ii) Mica Creek via Mount Isa (20°49'S 139°27'E), (iii) Boulia (22°55'S 139°55'E), (iv) 48km E. of Middleton (22°16'S 141°56'E), (v) 42 km N. of Barrow Creek (21°54'S 133°34'E), and (vi) Minilya River (23°49'S 114°00'E). Mean phrase repetition rates (PRR) for each recording are provided to the right of each plot for reference. Recordings (iv) and (v) illustrate the transition between the introductory component and the lilting component. The approximate point of this transition is indicated with a grey dashed line. Recordings (i) and (ii) were made with RS3 by A. Ewart, while (iii), (iv) and (vi) were made by K. Hill with RS4, and (v) was made by D. Marshall also using RS4 (see methods).

FIGURE 48 in A revision of the Pauropsalta annulata Goding & Froggatt species group (Hemiptera: Cicadidae) based on morphology, calling songs and ecology, with investigations into calling song structure, molecular phylogenetic relationships and a case of hybridisation between two subspecies

FIGURE 48. Waveform plots illustrating the lilting component of the male calling song of Pauropsalta inversa sp. nov. from six different localities, including: (i) Eidsvold (25°22'S 151°07'E), (ii) Mundubbera (25°35'S 151°18'E), (iii) Mount Hope (32°50'S 145°53'E), (iv) Goolgowi (33°59'S 135°43'E), (v) Clermont (22°50'S 147°38'E), and (vi) Mount Moffatt (24°52'S 148°01'E). Mean phrase repetition rates (PRR) for each recording are provided to the right of each plot for reference. Recordings (iii) and (iv) were made with RS5, while the remainder were made with RS1 (see methods).

FIGURE 44 in A revision of the Pauropsalta annulata Goding & Froggatt species group (Hemiptera: Cicadidae) based on morphology, calling songs and ecology, with investigations into calling song structure, molecular phylogenetic relationships and a case of hybridisation between two subspecies

FIGURE 44. Male calling song structure of Pauropsalta corymbiae sp. nov. illustrated in expanded waveform plots (explained in Fig. 8), showing both introductory and lilting components. The spectrogram at the bottom of the figure displays song frequency, with arrows indicating side bands. This specimen was recorded with RS3 (see methods) at Bull's Gully, Adavale (25°58'S 144°59'E) by A. Ewart.