Pituitary luteinizing hormone responses to single doses of exogenous GnRH in female social Cape ground squirrels exhibiting low reproductive skew

The Cape ground squirrel Xerus inauris is unusual among social mammals as it exhibits a low reproductive skew, being a facultative plural breeder with not all females breeding within a group. We investigated pituitary function to assess whether there was reproductive inhibition at the level of the pituitary and potentially the hypothalamus in breeding and non-breeding female Cape ground squirrels. We did so during the summer and winter periods by measuring luteinizing hormone (LH) responses to single doses of 2 g exogenous gonadotropin-releasing hormone (GnRH) and physiological saline administered to 42 females from 11 colonies. Basal LH concentrations of females increased in response to the GnRH challenge. Basal plasma LH concentrations were greater during winter, when most oestrus events are observed. However, we found no differences in plasma LH concentrations between breeding and non-breeding females. We showed that the anterior pituitary of non-breeding female ground squirrels is no less sensitive to exogenously administered GnRH than that of breeding females. We therefore concluded that the pituitary is no more active in breeding than non-breeding females. The lack of differentiation in response to GnRH suggests that either non-breeding females have ovaries that are less sensitive to LH or that they refrain from sexual activity with males through an alternative mechanism of self-restraint.     

Eavesdropping of an African ground squirrel on the heterospecific alarm calls of a noisy ground-nesting bird

Animals gather information about their environment from a variety of sources to enable adaptive decision-making behaviour. Eavesdropping on heterospecific alarm calls enhances predator avoidance, reduces time spent vigilant and allows for more time on daily activities such as foraging. If the information is relevant and reliable, individuals that respond to heterospecific signals may benefit from a wider range of information at a low marginal cost. The Cape ground squirrel (Xerus inauris) and crowned lapwing (Vanellus chilensis) are ground-dwelling species that are taxonomically distant but share similar predators, habitat and anti-predatory behaviours. We used playback experiments of the alarm calls produced by conspecifics and lapwings to investigate the vigilance responses of adult female Cape ground squirrels. Squirrels responded with greater vigilance to both squirrel and lapwing alarm calls, and no changes of vigilance levels were observed in response to a control sound. However, contrary to our predictions, changes in vigilance and time to relax did not differ between conspecific versus heterospecific playbacks. The results from our study suggest that squirrels perceive lapwing alarm calls as relevant and reliable information and that responding to it could increase their survival.     

Olfactory Snake‐Predator Discrimination in the Cape Ground Squirrel

Small mammals have a number of means to detect and avoid predators, including visual, auditory and olfactory cues. Olfactory cues are particularly important for nocturnal or fossorial species where visual cues would not be as reliable. The Cape ground squirrel (Xerus inauris) is a semi‐fossorial, diurnal mammal from southern Africa. Cape ground squirrels encounter multiple species of predatory snake that pursue individuals underground where visual and social cues are limited. We assessed whether Cape ground squirrels use odours to discriminate between snakes by presenting a non‐venomous snake, a venomous snake and a control odour collected on polyethylene cubes to 11 adult female squirrels from 11 different social groups. Cape ground squirrels responded by inspecting the cube, displaying snake harassment–associated behaviours and decreasing time spent in close proximity to snake odours when compared with a control. They also displayed discrimination between two snake species by increasing the frequency of cube inspection and increasing harassment behaviours with venomous snake odours when compared with non‐venomous snake odours. We conclude that Cape ground squirrels respond with snake‐specific antipredator behaviours when presented olfactory cues alone. Olfactory discrimination may be maintained by the decreased utility of other methods of predator detection: sight and group detection, in below‐ground encounters.     

Coalescent-Based Genome Analyses Resolve the Early Branches of the Euarchontoglires

Despite numerous large-scale phylogenomic studies, certain parts of the mammalian tree are extraordinarily difficult to resolve. We used the coding regions from 19 completely sequenced genomes to study the relationships within the super-clade Euarchontoglires (Primates, Rodentia, Lagomorpha, Dermoptera and Scandentia) because the placement of Scandentia within this clade is controversial. The difficulty in resolving this issue is due to the short time spans between the early divergences of Euarchontoglires, which may cause incongruent gene trees. The conflict in the data can be depicted by network analyses and the contentious relationships are best reconstructed by coalescent-based analyses. This method is expected to be superior to analyses of concatenated data in reconstructing a species tree from numerous gene trees. The total concatenated dataset used to study the relationships in this group comprises 5,875 protein-coding genes (9,799,170 nucleotides) from all orders except Dermoptera (flying lemurs). Reconstruction of the species tree from 1,006 gene trees using coalescent models placed Scandentia as sister group to the primates, which is in agreement with maximum likelihood analyses of concatenated nucleotide sequence data. Additionally, both analytical approaches favoured the Tarsier to be sister taxon to Anthropoidea, thus belonging to the Haplorrhine clade. When divergence times are short such as in radiations over periods of a few million years, even genome scale analyses struggle to resolve phylogenetic relationships. On these short branches processes such as incomplete lineage sorting and possibly hybridization occur and make it preferable to base phylogenomic analyses on coalescent methods.     

Seasonal patterns of body temperature daily rhythms in group-living Cape ground squirrels Xerus inauris

Organisms respond to cyclical environmental conditions by entraining their endogenous biological rhythms. Such physiological responses are expected to be substantial for species inhabiting arid environments which incur large variations in daily and seasonal ambient temperature (T(a)). We measured core body temperature (T(b)) daily rhythms of Cape ground squirrels Xerus inauris inhabiting an area of Kalahari grassland for six months from the Austral winter through to the summer. Squirrels inhabited two different areas: an exposed flood plain and a nearby wooded, shady area, and occurred in different social group sizes, defined by the number of individuals that shared a sleeping burrow. Of a suite of environmental variables measured, maximal daily T(a) provided the greatest explanatory power for mean T(b) whereas sunrise had greatest power for T(b) acrophase. There were significant changes in mean T(b) and T(b) acrophase over time with mean T(b) increasing and T(b) acrophase becoming earlier as the season progressed. Squirrels also emerged from their burrows earlier and returned to them later over the measurement period. Greater increases in T(b), sometimes in excess of 5°C, were noted during the first hour post emergence, after which T(b) remained relatively constant. This is consistent with observations that squirrels entered their burrows during the day to 'offload' heat. In addition, greater T(b) amplitude values were noted in individuals inhabiting the flood plain compared with the woodland suggesting that squirrels dealt with increased environmental variability by attempting to reduce their T(a)-T(b) gradient. Finally, there were significant effects of age and group size on T(b) with a lower and less variable T(b) in younger individuals and those from larger group sizes. These data indicate that Cape ground squirrels have a labile T(b) which is sensitive to a number of abiotic and biotic factors and which enables them to be active in a harsh and variable environment.     

The Social Organization of the Cape Ground Squirrel (Xerus inauris; Rodentia: Sciuridae)

The Cape ground squirrel (Xerus inauris) of southern Africa is a tropical species that does not hibernate. Field observations using scan and all-occurrence sampling revealed that this species was highly social. Female Cape ground squirrels formed social units of related females and their subadult young, as is typical for other ground squirrels. Female social groups were usually composed of 2–3 adult females and 2–3 subadults of either sex. Members of these female social groups shared sleeping burrows and feeding ranges. Female social groups did not cooperatively defend their feeding ranges from adjacent groups in other burrow clusters. Interactions within female social groups were highly amicable, and no dominance hierarchy was evident. Males in this species also lived in groups. These all-male bands of up to 19 individuals lived almost independently from female groups. The entire male band shared one home range, although ephemeral sub-bands were formed daily. The composition and size of these sub-bands changed daily. Interactions among males, which were largely amicable, included allogrooming and sleeping together. Analysis of interactions within the band indicated a stable, linear, dominance hierarchy among males. Dispersal in this species appeared to be male biased as is typical of other ground-dwelling squirrels, with males dispersing at reproductive maturity. Males joining male bands were thus dispersers and were not likely to be closely related. Sociality in the Cape ground squirrel may be summarized as highly social female kin clusters and associated social non-kin bands of males.     

Cape ground squirrels as ecosystem engineers: modifying habitat for plants,small mammals and beetles in Namib Desert grasslands

Burrowing and foraging of semi‐fossorial rodents can affect species distribution and composition. Ground squirrels dig large burrow systems for refuge from predators and temperature extremes. Burrowing and foraging around burrows by squirrels may affect habitat and resource distributions for other organisms. We examined the impact of Cape ground squirrels (Xerus inauris) on vegetation, small mammals and beetles during winter and summer in grasslands on the edge of the Namib Desert. At each burrow system and paired control site without burrows, we estimated plant cover and height using quadrats (N = 8 paired sites), small mammal abundance and species richness using mark‐recapture techniques (N = 8 paired sites) and beetle abundance and species richness using pitfall traps (N = 6 paired sites, winter only). Squirrel burrowing and foraging activities resulted in lower plant cover and height, higher small mammal abundance and lower beetle abundance and species richness. Squirrels also reduced more plant cover in winter compared to summer, but had no effect on small mammal species richness. Furthermore, plant cover and height were higher in summer, whereas small mammal abundance and species richness were higher in winter. Our results suggest that Cape ground squirrels are important ecosystem engineers that influence plant and animal communities in the Namib Desert grasslands.     

Karyotypic evolution of the family Sciuridae: inferences from the genome organizations of ground squirrels

Cross-species chromosome painting has made a great contribution to our understanding of the evolution of karyotypes and genome organizations of mammals. Several recent papers of comparative painting between tree and flying squirrels have shed some light on the evolution of the family Sciuridae and the order Rodentia. In the present study we have extended the comparative painting to the Himalayan marmot (Marmotahimalayana) and the African ground squirrel (Xerus cf. erythropus), i.e. representative species from another important squirrel group--the ground squirrels--, and have established genome-wide comparative chromosome maps between human, eastern gray squirrel, and these two ground squirrels. The results show that 1) the squirrels so far studied all have conserved karyotypes that resemble the ancestral karyotype of the order Rodentia; 2) the African ground squirrels could have retained the ancestral karyotype of the family Sciuridae. Furthermore, we have mapped the evolutionary rearrangements onto a molecular-based consensus phylogenetic tree of the family Sciuridae.     

The relative roles of the parasol-like tail and burrow shuttling in thermoregulation of free-ranging Cape ground squirrels,Xerus inauris

As small arid-zone mammals, Cape ground squirrels (Xerus inauris) are unusual in being diurnally active. It is postulated that they remain active during the day by using their parasol-like tails to shade their bodies whilst foraging. However, no studies have continuously measured body temperature to determine the effect of using the tail as a parasol, relative to other thermoregulatory behaviours, such as burrow retreat. We caught four free-ranging Cape ground squirrels (673 ± 36 g) and surgically implanted miniature temperature-sensitive data loggers into their abdomens, to record body temperature every 5 min to an accuracy of 0.04 °C, before they were released back into their home range and observed for two weeks. Mean daily peak black globe temperature was 41 °C, and daily peak body temperature reached 40 °C. Ground squirrels raised their tails significantly more often at globe temperatures above 30 °C, but raising the tail did not decrease body temperature, nor prevent body temperature rising. Ground squirrels retreated to burrows, at 18 °C, significantly more often at high body temperatures and body temperature dropped 1–2 °C before re-emergence. We believe that the tail was raised to provide thermal comfort during high solar radiation exposure, and that burrow retreat was employed to dissipate a heat load and remain active diurnally.     

Phylogeography of the Calonectris shearwaters using molecular and morphometric data

We investigated phylogenetic relationships and the biogeographic history of the Calonectris species complex, using both molecular and biometric data from one population of the Cape Verde shearwater Calonectris edwardsii (Cape Verde Islands), one from the streaked shearwater C. leucomelas (western Pacific Ocean) and 26 from Cory's shearwater populations distributed across the Atlantic (C. d. borealis) and the Mediterranean (C. d. diomedea). The streaked shearwater appeared as the most basal and distant clades, whereas the genetic divergences among the three main clades within the Palearctic were similar. Clock calibrations match the first speciation event within Calonectris to the Panama Isthmus formation, suggesting a vicariant scenario for the divergence of the Pacific and the Palearctic clades. The separation between the Atlantic and Mediterranean clades would have occurred in allopatry by range contraction followed by local adaptation during the major biogeographic events of the Pleistocene. The endemic form from Cape Verde probably evolved as a result of ecological divergence from the Mediterranean subspecies. Finally, one Mediterranean population (Almeria) was unexpectedly grouped into the Atlantic subspecies clade, both by genetic and by morphometric analyses, pointing out the Almeria-Oran oceanographic front (AOOF) as the actual divide between the two Cory's shearwater subspecies. Our results highlight the importance of oceanographic boundaries as potentially effective barriers shaping population and species phylogeographical structure in pelagic seabirds.     

The Adaptive Function of Masturbation in a Promiscuous African Ground Squirrel

Background

Studies of animal mating systems increasingly emphasize female multiple mating and cryptic sexual selection, particularly sperm competition. Males under intense sperm competition may manipulate sperm quantity and quality through masturbation, which could waste sperm and decrease fertility. I examined the factors influencing masturbation by male Cape ground squirrels (Xerus inauris) in light of a number of functional hypotheses.

Methodology

Observational data on a marked population of squirrels were collected in east-central Namibia using scan and all-occurrences sampling.

Findings

Masturbation was far more frequent on days of female oestrus and mostly occurred after copulation. Masturbation rates were higher in dominant males, which copulate more, than in subordinates and increased with number of mates a female accepts.

Conclusions

These results suggest that masturbation in this species was not a response to sperm competition nor a sexual outlet by subordinates that did not copulate. Instead masturbation could function as a form of genital grooming. Female Cape ground squirrels mate with up to 10 males in a 3-hr oestrus, and by masturbating after copulation males could reduce the chance of infection. Sexually transmitted infections (STIs) can profoundly affect fertility, and their consequences for mating strategies need to be examined more fully.     

Structure and allometry of genitalia in males and females of a social African ground squirrel with high polygynandry

The few studies that have looked at genital allometry in mammals have typically shown a positively allometric relationship with body size and high coefficients of variation. Cryptic female choice, sexual conflict or sperm competition are mechanisms underlying genital evolution and as these are not mutually exclusive, they are often difficult to disentangle. In addition, these mechanisms are affected by both male and female social structure and/or mating strategies and, as such, pre- and post-copulatory behaviours have been shown to alter selection on genitalia. We examined genital traits and allometry in a polygynandrous and social ground squirrel Xerus inauris . We found that male testes are positively allometric and account for 1.5% of their body weight, one of the highest percentages known for sciurids. The penis, at 42.4% of head/body length, was isometric while the female reproductive tract, 22.4% head/body length, demonstrated no such relationship. Based on the allometric relationships of both males and females presented here, in conjunction with high levels of competition for females and lack of male aggression and territoriality, we suggest that sperm competition is the most likely mechanism for the evolution of the extremely large genitalia in this species.     

Vigilance and grouping in the southern African ground squirrel (Xerus inauris)

Animals may form groups in response to the foraging–vigilance trade‐off, through enhanced predator detection (collective detection hypothesis) or reduced predation risk to the individual (dilution hypothesis), allowing individuals to decrease vigilance levels. Both hypotheses predict decreasing individual vigilance levels with increasing group size; however, the collective detection hypothesis also predicts increasing overall group vigilance with increasing group size. However, in species in which vigilance and foraging are not mutually exclusive, where vigilance may not be as costly, neither of these hypotheses may apply. Here, we examine the relationship between group size and vigilance in the social Cape ground squirrel (Xerus inauris), a species that can combine foraging and vigilance behaviours. Ten groups were observed using scan sampling, measuring both group and individual vigilance and group size. A negative relationship existed between individual vigilance and group size and a positive relationship between group vigilance and group size. Therefore, in Cape ground squirrels, vigilance seems to be costly even though it can be combined with foraging behaviours. Furthermore, group vigilance behaviour gives support to the collective detection hypothesis, whilst individual vigilance gives support to both hypotheses.     

Coalescence methods reveal the impact of vicariance on the spatial genetic structure of Elephantulus edwardii (Afrotheria, Macroscelidea)

Within the Macroscelidea 15 species of elephant-shrews are recognized, of which nine occur in the southern African subregion. The Cape rock elephant-shrew (Elephantulus edwardii) is the only strictly endemic South African elephant-shrew species. Recent distribution data suggest that E. edwardii is continuously distributed from Namaqualand in the Western Cape Province to Port Elizabeth in the Eastern Cape Province. Molecular sequences from the mitochondrial cytochrome b gene and variable control region indicate significant substructure within the Cape rock elephant-shrew across its distribution. Our data unequivocally showed the presence of a northern Namaqua and central Fynbos clade with four evolutionary lineages identified within the latter. The geographical delimitation of the northern and central clades corresponds closely with patterns reported for other rock-dwelling vertebrate species, indicating a shared biogeographical history for these taxa in South Africa. A coalescent method revealed the effects of ancestral polymorphism in shaping the Namaqua and Fynbos populations since their divergence ~1.7 million years ago. Furthermore, our analyses uncovered a distinct Karoo lineage(s) that does not correspond to any of the previously described and/or currently recognized species, and we therefore argue for the possible recognition of a new sister taxon to E. edwardii. The taxonomic affinities of this clade were examined by sequencing corresponding regions from the type specimens of species described in the past, but which presently are synonimized within E. edwardii. Our results reveal the morphological misidentification of one of these types, accentuating the problems of field identification.     

Phylogeography of the longhorn cactus beetle Moneilema appressum LeConte (Coleoptera: Cerambycidae): was the differentiation of the Madrean sky islands driven by Pleistocene climate changes?

Although it has been suggested that Pleistocene climate changes drove population differentiation and speciation in many groups of organisms, population genetic evidence in support of this scenario has been ambiguous, and it has often been difficult to distinguish putative vicariance from simple isolation by distance. The sky island communities of the American Southwest present an ideal system in which to compare late Pleistocene range fragmentations documented by palaeoenvironmental studies with population genetic data from organisms within these communities. In order to elucidate the impact of Pleistocene climate fluctuations on these environments, biogeographic patterns in the flightless longhorn cactus beetle, Moneilema appressum were examined using mitochondrial DNA sequence data. Gene tree relationships between haplotypes were inferred using parsimony, maximum-likelihood, and Bayesian analysis. Nested clade analysis, Mantel tests, and coalescent modelling were employed to examine alternative biogeographic scenarios, and to test the hypothesis that Pleistocene climate changes drove population differentiation in this species. The program mdiv was used to estimate migration and divergence times between populations, and to measure the statistical support for isolation over ongoing migration. These analyses showed significant geographic structure in genetic relationships, and implicated topography as a key determinant of isolation. However, although the coalescent analyses suggested that a history of past habitat fragmentation underlies the observed geographic patterns, the nested clade analysis indicated that the pattern was consistent with isolation by distance. Estimated divergence times indicated that range fragmentation in M. appressum is considerably older than the end of the most recent glacial, but coincided with earlier interglacial warming events and with documented range expansions in other, desert-dwelling species of Moneilema.     

Analysing disparity by applying combined morphological and molecular approaches to French and Japanese carabid beetles

The expression of morphological disparity within a clade is related to its history and to the environmental parameters within which it develops. Recent developments in geometric morphometries allow quantitative estimation of morphological disparity, and facilitate comparisons with genetic data intended to provide phylogenetic information. Such comparisons were made between two sets of ground beetle species from regions that differ biogeographically and environmentally: 12 post-glacial reinvading species from NE France; and 15 Japanese species less likely to be affected by the Pleistocene glacial events. Genetic relationships were inferred from mitochondrial DNA (ND5 gene). Morphological divergences among the species were analysed using Procrustes ver. 2.0, based on 64 landmarks (generalized analyses and computation of additive distance trees). The established morphospaces indicate distinct disparity patterns in France and Japan, even though the genetic data show that neither of the two sets arc monophyletic, and that they are in fact intermixed in the same clade. This discrepancy is partly related to the presence of extreme (elongated) morphologies in the Japanese set. But the stronger disparity observed amongjapanese species does not correspond to greater genetic differences. Those extreme morphologies appear to be related to the degree of endemicity of the species. The differences between the French and Japanese morphological patterns are discussed in the context of possible geographic factors and climatic changes during the Pleistocene.     

Energetic costs of parasitism in the Cape ground squirrel Xerus inauris

Parasites have been suggested to influence many aspects of host behaviour. Some of these effects may be mediated via their impact on host energy budgets. This impact may include effects on both energy intake and absorption as well as components of expenditure, including resting metabolic rate (RMR) and activity (e.g. grooming). Despite their potential importance, the energy costs of parasitism have seldom been directly quantified in a field setting. Here we pharmacologically treated female Cape ground squirrels (Xerus inauris) with anti-parasite drugs and measured the change in body composition, the daily energy expenditure (DEE) using doubly labelled water, the RMR by respirometry and the proportions of time spent looking for food, feeding, moving and grooming. Post-treatment animals gained an average 19g of fat or approximately 25kJd-1. DEE averaged 382kJd-1 prior to and 375kJd-1 post treatment (p>0.05). RMR averaged 174kJd-1 prior to and 217kJd-1 post treatment (p<0.009). Post-treatment animals spent less time looking for food and grooming, but more time on feeding. A primary impact of infection by parasites could be suppression of feeding behaviour and, hence, total available energy resources. The significant elevation of RMR after treatment was unexpected. One explanation might be that parasites produce metabolic by-products that suppress RMR. Overall, these findings suggest that impacts of parasites on host energy budgets are complex and are not easily explained by simple effects such as stimulation of a costly immune response. There is currently no broadly generalizable framework available for predicting the energetic consequences of parasitic infection.     

EVOLUTIONARY RELATIONSHIPS AMONG COLONIES OF COLUMBIAN GROUND SQUIRRELS AS SHOWN BY MITOCHONDRIAL DNA

Mitochondrial DNA (mtDNA) from 71 Columbian ground squirrels (Spermophilus columbianus) collected in 12 locations in western Canada were assayed for restriction-site variation with 10 endonucleases. Five of these endonucleases revealed variant patterns, and the composite genotypes were used to develop a linear transformation series among the mtDNA genotypes. Two of the four clones had a wide distribution, while the remaining two clones were geographically restricted. The mtDNA of Columbian ground squirrels was also compared to two other species of Sciuridae: Richardson's ground squirrels (S. richardsonii) and Arctic ground squirrels (S. parryii). Calculation of divergences from fragment length and restriction-site data indicated that Arctic ground squirrels and Richardson's ground squirrels were more closely related to each other than either was to Columbian ground squirrels. The transformation series among clones within the Columbian ground squirrels was rooted using Richardson's and Arctic ground squirrels as out-groups. From these data, we conclude that the colonization by female founders of Columbian ground squirrel populations occurred after deglaciation along the eastern ranges of the Rocky Mountains, while colonies on the western ranges may have been present before extensive deglaciation occurred, having existed in refugia in northwestern Alberta.     

Miocene diversification of an open‐habitat predatorial passerine radiation,the shrikes (Aves: Passeriformes: Laniidae)

Diversification of avifaunas associated with savannah and steppes appears to correlate with open habitats becoming available, starting in the Miocene. Few comparative analyses exist for families for which all species are predominantly adapted to these habitats. One such group is Laniidae (Passeriformes), which are small‐ to medium‐sized predatory passerines known for their distinctive behaviour of impaling prey. We used multispecies coalescent‐based and concatenation methods to provide the first complete species‐level phylogeny for this group, as well as an estimate of the timing of diversification. Our analyses indicate that Laniidae as currently delimited is not monophyletic, as the genus Eurocephalus is not closely related to the remaining species. The two species currently assigned to the monotypic genera Urolestes and Corvinella are part of the same clade as the Lanius species, and we propose that they are included in the genus Lanius, making Laniidae monogeneric. The initial diversification of the clade is inferred to have occurred very rapidly, starting about 7.2–9.1 million years ago, timing depending on calibration method, but in either case coinciding with the expansion of C4 grasses. An African origin is inferred in the biogeographic analysis. In the redefined Laniidae, cooperative breeding is inferred to be restricted to a single clade, characterized by gregarious behaviour and rallying. Migratory behaviour evolved multiple times within the family.     

Phylogeography of the genus Dasiphora (Rosaceae) in the Qinghai‐Tibetan Plateau: divergence blurred by expansion

Plateau uprisings and climatic oscillations are considered to have caused extensive allopatric divergences that account for the rich species diversity of the Qinghai‐Tibetan Plateau (QTP). However, secondary contact during range shifts in the Quaternary glacial cycles or inter‐uplift stages may have restored the gene flow between species and so counteracted these divergences, particularly in rapidly‐adapting dominant elements. We tested this hypothesis by determining the phylogeographical history of Dasiphora (Rosaceae), a genus of two species that are widely distributed on the QTP and co‐exist in numerous localities. We sequenced two chloroplast DNA fragments (rbcL, trnT‐L) for 559 individuals from 87 populations. Bayesian methods were used to identify phylogenetic relationships and to estimate divergence times. Demographic histories were inferred using neutrality tests, mismatch distribution analysis, and coalescent simulation. A total of 112 haplotypes that clustered into three major groups were identified. The formation of these groups and their subgroups was dated to between the Pliocene and the late Pleistocene. In addition, we found that some groups underwent multiple extensive expansions. Species‐specific haplotypes were identified for each species, although these haplotypes phylogenetically intermixed. These results suggest that recent plateau uplifts and climatic oscillations might have caused the deep divergences observed within this genus. However, later range expansions probably blurred these divergences and possible species boundaries. Our results shed new light on the complex evolutionary history of the QTP alpine plants. © 2014 The Linnean Society of London, Biological Journal of the Linnean Society, 2014, 111 , 777–788.