Phylogeography and palaeodistribution modelling of Nassauvia subgenus Strongyloma (Asteraceae): exploring phylogeographical scenarios in the Patagonian steppe

The Patagonian steppe is an immense, cold, arid region, yet phylogeographically understudied. Nassauvia subgen. Strongyloma is a characteristic element of the steppe, exhibiting a continuum of morphological variation. This taxon provides a relevant phylogeographical model not only to understand how past environmental changes shaped the genetic structure of its populations, but also to explore phylogeographical scenarios at the large geographical scale of the Patagonian steppe. Here, we (1) assess demographic processes and historical events that shaped current geographic patterns of haplotypic diversity; (2) analyze hypotheses of isolation in refugia, fragmentation of populations, and/or colonization of available areas during Pleistocene glaciations; and (3) model extant and palaeoclimatic distributions to support inferred phylogeographical patterns. Chloroplast intergenic spacers, rpl32–trnL and trnQ–5′rps16, were sequenced for 372 individuals from 63 populations. Nested clade analysis, analyses of molecular variance, and neutrality tests were performed to assess genetic structure and range expansion. The present potential distribution was modelled and projected onto a last glacial maximum (LGM) model. Of 41 haplotypes observed, ten were shared among populations associated with different morphological variants. Populations with highest haplotype diversity and private haplotypes were found in central‐western and south‐eastern Patagonia, consistent with long‐term persistence in refugia during Pleistocene. Palaeomodelling suggested a shift toward the palaeoseashore during LGM; new available areas over the exposed Atlantic submarine platform were colonized during glaciations with postglacial retraction of populations. A scenario of fragmentation and posterior range expansion may explain the observed patterns in the center of the steppe, which is supported by palaeomodelling. Northern Patagonian populations were isolated from southern populations by the Chubut and the Deseado river basins during glaciations. Pleistocene glaciations indirectly impacted the distribution, demography, and diversification of subgen. Strongyloma through decreased winter temperatures and water availability in different areas of its range.     

Phylogeographical structure inferred from cpDNA sequence variation of <Emphasis Type="Italic">Zygophyllum xanthoxylon</Emphasis> across north-west China

Zygophyllum xanthoxylon, a desert species, displaying a broad east–west continuous distribution pattern in arid Northwestern China, can be considered as a model species to investigate the biogeographical history of this region. We sequenced two chloroplast DNA spacers (psbK-psbI and rpl32-trnL) in 226 individuals from 31 populations to explore the phylogeographical structure. Median-joining network was constructed and analysis of AMOVA, SMOVA, neutrality tests and distribution analysis were used to examine genetic structure and potential range expansion. Using species distribution modeling, the geographical distribution of Z. xanthoxylon was modeled during the present and at the Last Glacial Maximum (LGM). Among 26 haplotypes, one was widely distributed, but most was restricted to either the eastern or western region. The populations with the highest levels of haplotype diversity were found in the Tianshan Mountains and its surroundings in the west, and the Helan Mountains and Alxa Plateau in the east. AMOVA and SAMOVA showed that over all populations, the species lacks phylogeographical structure, which is speculated to be the result of its specific biology. Neutrality tests and mismatch distribution analysis support past range expansions of the species. Comparing the current distribution to those cold and dry conditions in LGM, Z. xanthoxylon had a shrunken and more fragmented range during LGM. Based on the evidences from phylogeographical patterns, distribution of genetic variability, and paleodistribution modeling, Z. xanthoxylon is speculated most likely to have originated from the east and migrated westward via the Hexi Corridor.     

Multiple periglacial refugia in the Patagonian steppe and post‐glacial colonization of the Andes: the phylogeography of Calceolaria polyrhiza

Aim We perform a phylogeographical study of an endemic Patagonian herbaceous plant to assess whether geographical patterns of genetic variation correspond to in situ Pleistocene survival or to glacial retreat and post‐glacial expansion. We also seek to determine the locations of potential glacial refugia and post‐glacial colonization routes. Location Southern Andes and Patagonian steppe. Methods We used Calceolaria polyrhiza, a widely distributed Patagonian herbaceous plant that occurs mainly in the understorey of Nothofagus rain forests and in the arid Patagonian steppe, as our model system. The chloroplast intergenic spacer trnH–psbA was sequenced for 590 individuals from 68 populations. Sequence data were analysed using phylogenetic (maximum parsimony, maximum likelihood and Bayesian inference) and population genetic (spatial analyses of molecular variance, mismatch distributions and neutrality tests) methods. Nested clade phylogeographic analyses, and divergence time estimates using a calibrated molecular clock, were also conducted. Results A total of 27 haplotypes identified in the present study clustered into four primary genealogical lineages, revealing three significant latitudinal phylogeographical breaks. The two high Andean lineages probably split first, during the late Miocene, and the Patagonian lineage split around 4 Ma, coincident with the establishment of the Patagonian steppe. Within each haplogroup, major diversification occurred in the Pleistocene. The Patagonian groups show a pattern consistent with a rapid post‐glacial expansion and colonization of the Andean flanks, achieved independently by four lineages. The highest haplotype diversity was found along a longitudinal transect that is remarkably congruent with the limit of the ice‐sheet extension during the Greatest Patagonian Glaciation. A north‐east expansion is evident, which is probably associated with the ‘Arid Diagonal’ fluctuations. Main conclusions Glacial climate fluctuations had a substantial impact on the diversification, distribution and demography of the study species. A scenario of multiple periglacial Pleistocene refugia and subsequent multiple recolonization routes, from eastern Patagonia to the Andean flanks, may explain the phylogeographical patterns observed. However, current genetic structure also preserves the imprints of older events that probably occurred in the Miocene and Pliocene, providing evidence that multiple processes, operating at different spatial and temporal scales, have moulded biodiversity in Patagonia.     

Living in a world of fire: the population dynamics of Mulinum spinosum in Northwestern Patagonia grasslands

Questions

How do fire frequency and fire size affect the long-term population dynamics of Mulinum spinosum? Which demographic parameters contribute most to the overall effect of fire on population growth? What is the relative importance of resprouting in sustaining population increase?

Location

Grass-shrub northwestern Patagonian steppe, Argentina.

Methods

We monitored five permanent plots excluded from grazing for 6 years. We measured shrub abundance, dimensions, reproductive status, seedling emergence, and the size structure of M. spinosum, a resprouting native shrub inhabiting the northwest Patagonian steppe. Data were used to parametrize a stochastic matrix model developed to explore the influence of fire frequency and fire size on long-term population dynamics. We analyzed hypothetical scenarios that included fire frequencies ranging from one per year up to exclusion.

Results

Except for annual fires, projections show growing populations regardless of fire frequency. For fire return intervals greater than 50 years, the population becomes independent of fires, with an annual population growth rate of 5.6%. The results suggest two relevant aspects of the population dynamics of this species: M. spinosum is well adapted to the current fire frequency and its resprouting capability will allow M. spinosum to survive and persist in the community, even under frequent fires.

Conclusions

Climate change models forecast an increase in summer temperature in NW Patagonia and, consequently, an enhanced fire frequency. Fire is a driver of M. spinosum encroachment that gets worse in overgrazed grasslands. Mulinum spinosum encroachment derivate in a relative replacement of palatable grasses by shrubs changes the ecosystem functionality and reduces productivity. Controlling this process is highly difficult and we suggest a change in the land use for the areas already deteriorated.

     

Tabula rasa in the Patagonian Channels? The phylogeography of Oreobolus obtusangulus (Cyperaceae)

The extent of the Pleistocene glaciations in the Patagonian Channel region (southwesternmost South America) and their impact on the vegetation there are largely unknown. Whether the regional flora was wiped out completely (tabula rasa) or survived in ice‐free pockets (in situ survival) is still an open question. The molecular imprint of either scenario should still be visible in extant populations. Therefore, DNA sequence data of Oreobolus obtusangulus Gaudich. (Cyperaceae) were analysed. This species is an abundant constituent of Patagonian cushion peat bogs, one of the Patagonian Channel region's major vegetation types. Three hundred and eighty‐four individuals from 48 populations were sequenced for two chloroplast (ycf3‐psaA and trnQ^UUG‐psbK intergenic spacers) and 14 nuclear loci containing simple sequence repeats (SSRs; microsatellites). Phylogenetic reconstructions and the geographic distribution of genetic diversity revealed that the species was split into three main lineages whose general distributions comprise three separate major regions, that is, south‐central Chile, Fuego‐Patagonia and the East Patagonian Andes, which probably constitute glacial refugia. Postglacial migration fronts formed a suture zone with high levels of genetic diversity in the Northwest Patagonian Andes, where remnants of a supposedly ancestral lineage were also found to be locally restricted to a single population (Huinay). The heavily glaciated Patagonian Channels were likely recolonized from the northwest, and partly from the south. Although the westernmost Patagonian Channel population (Estero Bachem) harboured private SSR alleles (singletons) and showed slightly elevated genetic diversity, it remained unclear whether this population actually survived in situ. This study helps fill a major gap in reconstructing the Pleistocene vegetation history of West and Andean Patagonia.     

History and evolution of alpine plants endemic to the Qinghai-Tibetan Plateau: Aconitum gymnandrum (Ranunculaceae)

How Quaternary climatic oscillations affected range distributions and intraspecific divergence of alpine plants on the Qinghai‐Tibetan Plateau (QTP) remains largely unknown. Here, we report a survey of chloroplast DNA (cpDNA) and nuclear ribosomal internal transcribed spacer (ITS) DNA variation aimed at exploring the phylogeographical history of the QTP alpine endemic Aconitum gymnandrum. We sequenced three cpDNA fragments (rpl20–rps12 intergenic spacer, the trnV intron and psbA‐trnH spacer) and also the nuclear (ITS) region in 245 individuals from 23 populations sampled throughout the species’ range. Two distinct lineages, with eastern and western geographical distributions respectively, were identified from a phylogenetic analysis of ITS sequence variation. Based on a fast substitution rate, these were estimated to have diverged from each other in the early Pleistocene approximately 1.45 Ma. The analysis of cpDNA variation identified nine chlorotypes that clustered into two major clades that were broadly congruent in geographical distribution with the two ITS lineages. The east–west split of cpDNA divergence was supported by an amova which partitioned approximately half of the total variance between these two groups of populations. Analysis of the spatial distribution of chlorotypes showed that each clade was subdivided into two groups of populations such that a total of four population groups existed in the species. It is suggested that these different groups derive from four independent glacial refugia that existed during the Last Glacial Maximum (LGM), and that three of these refugia were located at high altitude on the QTP platform itself at that time. Coalescent simulation of chlorotype genealogies supported both an early Pleistocene origin of the two main cpDNA clades and also the ‘four‐refugia’ hypothesis during the LGM. Two previous phylogeographical studies of QTP alpine plants indicated that such plants retreated to refugia at the eastern/south‐eastern plateau edge during the LGM and/or previous glacial maxima. However, the results for A. gymnandrum suggest that at least some of these cold‐tolerant species may have also survived centrally on the QTP platform throughout the Quaternary.     

Phylogeographic analysis of the endemic species Sibiraea angustata reveals a marginal refugium in the Qinghai–Tibet Plateau

The phylogeography of Sibiraea angustata, an endemic shrub species, was studied in the Qinghai–Tibet plateau (QTP). We investigated 466 individuals of S. angustata from 39 populations basically covering its total distribution area. Eight haplotypes (A–H) were detected by sequencing the intergenic chloroplast spacer trnS–trnG (600 bp), and one ancestral haplotype (A) was found to be widely distributed. The level of differentiation among populations was very high (G_ST=0.768; N_ST=0.850) and a significant phylogeographical structure was revealed (N_ST>G_ST). Analysis of molecular variance (AMOVA) similarily revealed a high level of differentiation among populations (84%, F_ST=0.842), indicating that little gene flow has occurred among populations mutually isolated by high mountains and rivers in the QTP. On the QTP platform there was only one widespread haplotype (A) in most populations, while populations along the eastern and southeastern edges had high diversity and unique haplotypes. Our results suggest that a glacial refugium may have been located on the eastern or southeastern edges of QTP during the last glaciation, and that interglacial and postglacial range expansion occurred from that refugium. Nested clade analysis (NCA) also suggests this scenario, which indicates that the current spatial distribution of cpDNA haplotypes and populations mainly resulted from long distance colonization, possibly coupled with subsequent or past fragmentation followed by range expansion and allopatric fragmentation.     

Phylogeographical structure in the coastal species Senecio rodriguezii (Asteraceae), a narrowly distributed endemic Mediterranean plant

Aim Our goals were (1) to assess the levels of chloroplast DNA variation in a narrowly distributed plant restricted to continental islands, (2) to ascertain whether a phylogeographical structure is present in plants restricted to coastal linear systems, and (3) to interpret the results in the light of the known palaeogeography of these islands. Location The Eastern Balearic Islands (Majorca and Minorca) in the Western Mediterranean Basin. Methods Sampling included 134 individuals from 28 populations of Senecio rodriguezii covering the entire range of the species. Sequences of the chloroplast genome (trnT–trnL spacer) were obtained and parameters of population genetic diversity and substructure were determined (h_sh_t, G_st). The geographical structure of genetic variation was assessed by an analysis of molecular variance (AMOVA). Additionally, a spatial AMOVA (SAMOVA) was used to identify groups of populations that were geographically homogeneous and maximally differentiated from each other. Finally, a pattern of isolation by distance was assessed by testing the correlation between the matrix of pairwise Φ_ST values and the matrix of geographical distances between pairs of populations using a Mantel test. Results Seven haplotypes were detected in S. rodriguezii. Only two of them were shared between islands; all of the others were restricted to Majorca (two) or Minorca (three). Overall, we found high levels of genetic diversity and significant geographical structuring of cpDNA markers. Most of the variation detected can be attributed to differences among populations (84.6%), but there was also a significant differentiation between the islands. Main conclusions Our results support the view that the Balearic Islands constitute a reservoir of genetic diversity, not only for widespread Mediterranean taxa, but also for endemic ones. The intraspecific genetic structure found in S. rodriguezii suggests that its population history was dominated by both expansion and contraction events. This has resulted in a species that is highly structured genetically, showing very few shared haplotypes between islands, and a high number of haplotypes restricted to small geographical areas within the islands. Changes in habitat availability and dynamic processes of population fragmentation and connectivity due to repeated cycles of sea‐level changes during the Quaternary are the possible underlying factors that have shaped the cpDNA pool of this endemic species on a regional scale.     

Phylogeographic structure of Hippophae tibetana (Elaeagnaceae) highlights the highest microrefugia and the rapid uplift of the Qinghai‐Tibetan Plateau

The uplift of the Qinghai‐Tibetan Plateau (QTP) dramatically changed the topography and climate of Asia and affected the biodiversity of the plateau and its adjacent areas. However, the effects of the uplift on the dispersal, differentiation and adaptation of plants remain a puzzle when the date and processes of the uplift cannot be determined with certainty and the impacts of the Quaternary glaciations on plants on the QTP are unknown. To clarify the relationships among plants on the QTP with the plateau uplift and the Quaternary glaciations, the cpDNA trnT‐trnF regions of 891 individuals from 37 populations of Hippophae tibetana, endemic to the QTP, were sequenced in the present study. A total of 50 haplotypes were found and a strong phylogeographic structure was revealed (N_ST = 0.854, G_ST = 0.611, N_ST > G_ST, P < 0.01). The results show that three main lineages of the present populations of H. tibetana occupy the western, the middle, and the eastern geographical range, respectively, and their divergence time dates back to 3.15 Ma before present. Of 50 haplotypes, 33 (66%) are private haplotypes, which are restricted to single populations. These private haplotypes are scattered throughout the present geographical range of H. tibetana and originated from multiple differentiations in many lineages during more than 1.0 Ma period, strongly suggesting that multiple microrefugia of H. tibetana existed throughout the present geographical range during the last glacial maximum (LGM) and even earlier glaciations. Additionally, the average elevation of present populations is over 4500 m in the west and the equilibrium‐line of glaciers in the LGM was 500–300 m lower than present in the major interior part of the plateau suggesting that at most sites in the west, LGM microrefugia of H. tibetana may have been above 4000 m above sea level, the highest of all known refugia. Moreover, the divergence times among and within the three lineages and their distinct distributions as well as dispersal barriers support the theory of the recent and rapid uplift of the QTP. The rapid uplift of the plateau within the last 3.4 Ma and the associated environmental changes may have affected the dispersal and differentiation of H .tibetana and shaped its phylogeographic structure.     

Phylogeography of rare fern <Emphasis Type="Italic">Polystichum glaciale</Emphasis> endemic to the subnival zone of the Sino-Himalaya

Previous phylogeographical studies of the Sino-Himalaya (SH) regions have mainly focused on seed plants from forest or alpine grassland habitats, whereas the flora of the subnival summits, especially the ferns, has largely been ignored. Here, we report on phylogeographical studies on Polystichum glaciale, a rare fern endemic to the subnival belt of the SH region. Based on cpDNA/nDNA sequences, strikingly rich genetic diversity was detected in P. glaciale. Combined with the lack of ‘isolation by distance’ and the major genetic differentiation among populations revealed by AMOVA, they collectively suggested that P. glaciale exhibited island-like population genetic structure. Phylogeographical structure with two genetic groups (N vs. S) was further identified in P. glaciale by the SAMOVA based on cpDNA data, of which the geographical pattern was mainly associated with the biogeographical boundary between the northern and southern Hengduan Mountains at 29°N latitude. We concluded that extremely complex topography of SH region and highly fragmented subnival habitat have played a critical role in shaping phylogeographical structure and genetic differentiation of P. glaciale. Mismatch distribution analyses and ecological niche modelling suggested P. glaciale has undergone north-westward retreat after the LGM. Predictions of its future distribution indicated the possibility of compression within suitable subnival habitats. We suggest in situ conservation should be urgently implemented to preserve this rare fern. Our results represent a first framework for a comprehensive understanding of the biogeographical history of fern species associated with the subnival belt of the SH region and the effects of historical events on its genetic architecture.     

Phylogenetic relationships and intraspecific diversity of a North Patagonian Fescue: evidence of differentiation and interspecific introgression at peripheral populations

Peripheral sites usually offer suboptimal conditions for species with wide distributions, where expression of phenotypic variability and potential interspecific hybridization might be enhanced. The Patagonian steppe, the largest and southernmost dryland ecosystem in South America, is characterized by natural rangelands dominated by grasses. Festuca pallescens is a keystone species with a wide distribution in Patagonia over diverse environments reaching the extreme arid zones in the Somuncura plateau, a biogeographical island. Our aim is to study the phylogenetic relationships among Festuca pallescens populations as well as between this species and the sympatric F. argentina in North Patagonia. We analysed fourteen populations along a west-east transect of about 500 km in North Patagonia with three types of molecular markers: ITS, chloroplast trnL-F and eight nuclear microsatellites. Bayesian inferences, maximum parsimony and maximum likelihood analyses with trnL-F and ITS showed that F. pallescens is related to the Patagonian clade within the Festuca phylogeny. However, the easternmost populations of F. pallescens at Somuncura plateau were highly differentiated from the other populations and clustered with F. argentina (a sympatric species of the Asian-American clade). Principal coordinates analyses and Bayesian clustering performed with nuclear microsatellites as well as morphoanatomical traits, showed an intermediate position of one of these easternmost populations with respect to the two species, suggesting admixture. The high genetic variability observed in these peripheral populations highlight their relevance for conservation and might be indicating the existence of evolutionary processes triggering events of speciation in the Patagonian fescues.     

Phylogeographic analyses suggest that a deciduous species (Ostryopsis davidiana Decne., Betulaceae) survived in northern China during the Last Glacial Maximum

Aim Palaeontologial data suggest that all temperate forest species in northern China migrated southwards during the Last Glacial Maximum (LGM) and recolonized post‐glacially within the Holocene. We tested this assumption using phylogeographical studies of a temperate deciduous shrub species (Ostryopsis davidiana Decne., Betulaceae), which has a wide distribution in northern China. Location Northern China. Methods We sequenced two chloroplast DNA (cpDNA) fragments (trnL–trnF and psbA–trnH, together about 1300 bp in length) of 294 plants from 21 populations across the total distribution range of this species. We used maximum parsimony and haplotype network methods to construct phylogenetic relationships among haplotypes. Results The analysis of cpDNA variation identified eight haplotypes. A single haplotype was fixed in all populations except for one population that was polymorphic, having two haplotypes. The population subdivisions were extremely high (G_ST = 0.972 and N_ST = 0.974), suggesting very low gene flow between populations. Haplotypes clustered into two tentative clades, both of which occur in the southern region of the species’ range but only one of which occurs in the northern region. Across the sampled populations, the haplotype distributions were differentiated geographically. Main conclusions Our analyses suggest that multiple refugia were maintained across the range of O. davidiana in both northern (north of the Qing Mountains) and southern (south of the Qing Mountains) regions during the LGM rather than that the species survived only in the south and subsequently colonized northwards. The extremely low within‐population diversity of this species suggests strong bottleneck or founder effects within each fragmented region during the Quaternary climatic oscillations. These findings provide important clues for understanding range shifts and changes in within‐ and/or between‐population genetic diversity of temperate forests in response to past climatic oscillations in northern China.     

Variation in the chloroplast DNA of Swiss stone pine (Pinus cembra L.) reflects contrasting post-glacial history of populations from the Carpathians and the Alps

Aim To characterize the genetic structure and diversity of Pinus cembra L. populations native to two disjunct geographical areas, the Alps and the Carpathians, and to evaluate the rate of genetic differentiation among populations. Location The Swiss Alps and the Carpathians. Methods We screened 28 populations at three paternally inherited chloroplast simple sequence repeats (cpSSRs) for length variation in their mononucleotide repeats. Statistical analysis assessed haplotypic variation and fixation indices. Hierarchical analysis of molecular variance (AMOVA), Mantel test, spatial analysis of molecular variance (SAMOVA) and barrier analyses were applied to evaluate the geographical partitioning of genetic diversity across the species’ range. Results Haplotypic diversity was generally high throughout the natural range of P. cembra, with the mean value substantially higher in the Carpathians (H = 0.53) than in the Alps (H = 0.35). The isolated Carpathian populations showed the highest haplotype diversity among the populations originating from the High Tatras (Velka Studena Dolina) and South Carpathians (Retezat Mountains). AMOVA revealed that only 3% of the total genetic variation derived from genetic differentiation between the two mountain ranges. Differentiation among Carpathian populations was higher (F_ST = 0.19) than among Alpine populations (F_ST = 0.04). Low, but significant, correlation was found between the geographical and genetic distances among pairs of populations (r = 0.286, P < 0.001). SAMOVA results revealed no evident geographical structure of populations. barrier analysis showed the strongest differentiation in the eastern part of the species’ range, i.e. in the Carpathians. Main conclusions The populations of P. cembra within the two parts of the species’ range still share many cpDNA haplotypes, suggesting a common gene pool conserved from a previously large, continuous distribution range. Carpathian populations have maintained high haplotypic variation, even higher than Alpine populations, despite their small population sizes and spatial isolation. Based on our results, we emphasize the importance of the Carpathian populations of Swiss stone pine for conservation. These populations comprise private haplotypes and they may represent a particular legacy of the species’ evolutionary history.     

Extensive population expansion of Pedicularis longiflora (Orobanchaceae) on the Qinghai‐Tibetan Plateau and its correlation with the Quaternary climate change

The Qinghai‐Tibetan Plateau (QTP) is thought to be more strongly affected by the Quaternary glaciations than most other regions of the same latitude. It would be of great interest to investigate the population genetic structure of organisms distributed on the platform and its correlation with the Quaternary climatic oscillations. Here we used the chloroplast (cp)DNA trnT‐trnF sequence to study genetic variation and phylogeography of Pedicularis longiflora, an alpine herb with extensive distribution on the QTP. Based on a range‐wide sampling comprising 41 populations and 910 individuals, we detected 30 cpDNA haplotypes that were divided into five clades by phylogenetic and network analyses and a strong phylogeographical structure. All haplotypes but one in the three basal clades occur exclusively in the southeast QTP, whereas haplotypes in the young clade V occupy almost the whole species range. In particular, the young haplotype H18 occurs in 420 individuals, even at a frequency of 100% in some QTP platform populations and the Altai population. The haplotype distribution pattern, together with molecular clock estimation and mismatch distribution analysis, suggests that the southeast QTP was either a refuge for P. longiflora during the Quaternary climatic change or is the place of origin of the species. The present wide distribution of the species on the QTP platform has resulted from recent population expansions which could be dated back to 120 000–17 000 years ago, a period mostly before the last glacial maximum. The possible relationships among geographic genetic structure, climatic change and species diversification in Pedicularis are also discussed.     

Multilocus phylogeography of the Patagonian lizard complex Liolaemus kriegi (Iguania: Liolaemini)

This study presents a detailed phylogeographical analysis of one of the most conspicuous groups of lizards in northwestern Patagonia, the Liolaemus kriegi complex. This region is geographically very complex as a result of Andean orogeny and subsequent volcanism coupled with a long history of glaciations and climatic changes. For 247 individuals we sequenced one mitochondrial gene (cytochrome b) and for a subset we sequenced another mitochondrial gene [12S ribosomal RNA (12S)] and two nuclear fragments [kinesin family member 24 (KIF24) and BA3 ribosomal RNA (BA3)]. We obtained gene trees and mitochondrial and nuclear haploytpe networks, and estimated genetic distances between the main lineages and basic molecular diversity indices. We also performed spatial analysis of molecular variance (SAMOVA) and Bayesian Skyline Plot (BSP) analyses, and concordant patterns from different lines of evidence permitted delimitation of seven lineages: two described species, Liolaemus buergeri and Liolaemus tregenzai; four candidate species, Liolaemus sp. A, Liolaemus sp. B, Liolaemus sp. C, and Liolaemus sp. D; and one lineage that includes all individuals from the geographical range of Liolaemus ceii and L. kriegi, referred to as L. kriegi + L. ceii. We discuss the evolutionary processes that may contribute to the origin of these lineages and their taxonomic and conservation implications. © 2014 The Linnean Society of London, Biological Journal of the Linnean Society, 2014, 113 , 256–269.     

Chloroplast phylogeography of <Emphasis Type="Italic">Helianthemum songaricum</Emphasis> (Cistaceae) from northwestern China: implications for preservation of genetic diversity

Two chloroplast intergenic spacers (trnD-trnT and rps16-trnK) were used to study the phylogeographical structure of Helianthemum songaricum in northwestern China, with 12 haplotypes detected. Phylogenetic analysis showed that H. songaricum comprised two lineages, one distributed in the Yili Valley and the other in the western Ordos Plateau. Nested clade phylogeographic analysis likewise indicated that haplotypes in the Yili Valley and those in the western Ordos Plateau formed sister monophyletic clades. This lineage split was also supported by AMOVA analysis and the Mantel test. AMOVA showed that 99.41% of variance in H. songaricum occurred between the two distribution regions, and correlation between genetic differentiation and geographical distances was significant (r ² = 0.877, P < 0.0001). All populations in the Yili Valley shared haplotype A with high frequency, and range expansion was detected by nested clade analysis and strongly supported by negative Fu’s F _S-values, Tajima’s D-values, and mismatch distribution analysis. We speculate that aggravation of the dry and cold climate during the early Quaternary, combined with plant physiological features, were determining factors contributing to the lineage split, and climate oscillations most likely led to the Yili range expansion. The high drift load (F _ST = 0.9923, G _ST = 0.663) and inbreeding load (H _S = 0.219) of H. songaricum indicate a significant extinction risk, and protective measures should be taken immediately.     

Phylogeography of Pinus tabulaeformis Carr. (Pinaceae), a dominant species of coniferous forest in northern China

How coniferous trees in northern China changed their distribution ranges in response to Quaternary climatic oscillations remains largely unknown. Here we report a study of the phylogeography of Pinus tabulaeformis, an endemic and dominant species of coniferous forest in northern China. We examined sequence variation of maternally inherited, seed‐dispersed mitochondrial DNA (mtDNA) (nad5 intron 1 and nad4/3–4) and paternally inherited, pollen‐ and seed‐dispersed chloroplast DNA (cpDNA) (rpl16 and trnS‐trnG) within and among 30 natural populations across the entire range of the species. Six mitotypes and five chlorotypes were recovered among 291 trees surveyed. Population divergence was high for mtDNA variation (G_ST = 0.738, N_ST = 0.771) indicating low levels of seed‐based gene flow and significant phylogeographical structure (N_ST > G_ST, P < 0.05). The spatial distribution of mitotypes suggests that five distinct population groups exist in the species: one in the west comprising seven populations, a second with a north–central distribution comprising 15 populations, a third with a southern and easterly distribution comprising five populations, a fourth comprising one central and one western population, and a fifth comprising a single population located in the north‐central part of the species’ range. Each group apart from the fourth group is characterized by a distinct mitotype, with other mitotypes, if present, occurring at low frequency. It is suggested, therefore, that most members of each group apart from Group 4 are derived from ancestors that occupied different isolated refugia in a previous period of range fragmentation of the species, possibly at the time of the Last Glacial Maximum. Possible locations for these refugia are suggested. A comparison of mitotype diversity between northern and southern subgroups within the north‐central group of populations (Group 2) showed much greater uniformity in the northern part of the range both within and between populations. This could indicate a northward migration of the species from a southern refugium in this region during the postglacial period, although alternative explanations cannot be ruled out. Two chlorotypes were distributed across the geographical range of the species, resulting in lower levels of among‐population chlorotype variation. The geographical pattern of variation for all five chlorotypes provided some indication of the species surviving past glaciations in more than one refugium, although differentiation was much less marked, presumably due to the greater dispersal of cpDNA via pollen.     

Multiple glacial refugia and postglacial colonization routes inferred for a woodland geophyte,Cyclamen purpurascens: patterns concordant with the Pleistocene history of broadleaved and coniferous tree species

The phylogeographical history of mid‐altitude woodland herbs that depend on moist and shaded forest habitats is poorly understood. Here, we analysed the genetic structure of Cyclamen purpurascens, a mountainous calcicolous perennial, to test hypotheses regarding its glacial survival in single or multiple refugia and postglacial colonization routes, and to explore how they are congruent with the histories inferred for temperate trees and other mountainous herbs. We gathered AFLP data and chloroplast DNA sequences (trnD‐trnT region) from 68 populations spanning the entire distribution range (the Jura Mountains, Alps, western Carpathians, Dinarides). Both genetic markers revealed two main phylogeographical groups (phylogroups) in C. purpurascens. Additionally, AFLP data detected a more detailed structure of five phylogroups: two widespread, showing east?west geographical separation, and three local ones, restricted to somewhat disjunct, marginal regions of the species range. We suggest that C. purpurascens survived the last glaciation in two main regions, the foothills of the Southern Limestone Alps and the Karst area of the north‐western Dinarides, and possibly also in microrefugia in the Western Carpathians. The glacial persistence and colonization routes of this woodland herb are highly concordant with those inferred for several temperate trees, especially the European beech. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, 105 , 741–760.     

Population genetic structure and historical population dynamics of the South American sea lion, <Emphasis Type="Italic">Otaria flavescens</Emphasis>, in north-central Patagonia

The north-central Patagonian coast is the sea lions most abundant area in Argentina. As occurs along the entire Atlantic coast, the distribution of breeding colonies at this smaller geographical scale is also patchy, showing at least three areas with breeding activity. We study the genetic structure and historical population dynamics of the species in five colonies in this area, analysing a 508 base-pair segment of the D-loop control region. Otaria flavescens showed 10 haplotypes with 12 polymorphic sites. The genealogical relationship between haplotypes revealed a shallow pattern of phylogeographic structure. The analysis of molecular variance showed significant differences between colonies, however, pairwise comparisons only indicate significant differences between a pair of colonies belonging to different breeding areas. The pattern of haplotype differentiation and the mismatch distribution analysis suggest a possible bottleneck that would have occurred 64,000 years ago, followed by a demographic expansion of the three southernmost colonies. Thus, the historical population dynamics of O. flavescens in north-central Patagonia appears to be closely related with the dynamics of the Late Pleistocene glaciations.     

Conservation genetics and geographic patterns of genetic variation of the endangered officinal herb Fritillaria pallidiflora

Fritillaria pallidiflora is an endangered officinal herb distributed in the Tianshan Mountains of northwestern China. We examined its phylogeography to study evolutionary processes and suggest implications for conservation. Six haplotypes were detected based on three chloroplast non‐coding spacers (psbA‐trnH, rps16, and trnS‐trnG); genetic variation mainly occurred among populations and SAMOVA groups. This species is distributed in different deep valleys, and we speculate that these fragmented habitats cause gene flow barriers among populations and groups. We also speculate that during glacial periods, extremely low temperatures and aridity caused additional range shrinkage and fragmentation, factors consequently resulting in significant intraspecific differentiation in allopatric regions. For setting a conservation management plan, we identified the Lucaogou region as the most important area, and we designated two ESUs for separate management.