Classification tree and minimum-volume ellipsoid analyses of the distribution of ponderosa pine in the western USA

Aim Ponderosa pine (Pinus ponderosa Douglas ex Lawson & C. Lawson) is an economically and ecologically important conifer that has a wide geographic range in the western USA, but is mostly absent from the geographic centre of its distribution – the Great Basin and adjoining mountain ranges. Much of its modern range was achieved by migration of geographically distinct Sierra Nevada (P. ponderosa var. ponderosa) and Rocky Mountain (P. ponderosa var. scopulorum) varieties in the last 10,000 years. Previous research has confirmed genetic differences between the two varieties, and measurable genetic exchange occurs where their ranges now overlap in western Montana. A variety of approaches in bioclimatic modelling is required to explore the ecological differences between these varieties and their implications for historical biogeography and impending changes in western landscapes. Location Western USA. Methods We used a classification tree analysis and a minimum‐volume ellipsoid as models to explain the broad patterns of distribution of ponderosa pine in modern environments using climatic and edaphic variables. Most biogeographical modelling assumes that the target group represents a single, ecologically uniform taxonomic population. Classification tree analysis does not require this assumption because it allows the creation of pathways that predict multiple positive and negative outcomes. Thus, classification tree analysis can be used to test the ecological uniformity of the species. In addition, a multidimensional ellipsoid was constructed to describe the niche of each variety of ponderosa pine, and distances from the niche were calculated and mapped on a 4‐km grid for each ecological variable. Results The resulting classification tree identified three dominant pathways predicting ponderosa pine presence. Two of these three pathways correspond roughly to the distribution of var. ponderosa, and the third pathway generally corresponds to the distribution of var. scopulorum. The classification tree and minimum‐volume ellipsoid model show that both varieties have very similar temperature limitations, although var. ponderosa is more limited by the temperature extremes of the continental interior. The precipitation limitations of the two varieties are seasonally different, with var. ponderosa requiring significant winter moisture and var. scopulorum requiring significant summer moisture. Great Basin mountain ranges are too cold at higher elevations to support either variety of ponderosa pine, and at lower elevations are too dry in summer for var. scopulorum and too dry in winter for var. ponderosa. Main conclusions The classification tree analysis indicates that var. ponderosa is ecologically as well as genetically distinct from var. scopulorum. Ecological differences may maintain genetic separation in spite of a limited zone of introgression between the two varieties in western Montana. Two hypotheses about past and future movements of ponderosa pine emerge from our analyses. The first hypothesis is that, during the last glacial period, colder and/or drier summers truncated most of the range of var. scopulorum in the central Rockies, but had less dramatic effects on the more maritime and winter‐wet distribution of var. ponderosa. The second hypothesis is that, all other factors held constant, increasing summer temperatures in the future should produce changes in the distribution of var. scopulorum that are likely to involve range expansions in the central Rockies with the warming of mountain ranges currently too cold but sufficiently wet in summer for var. scopulorum. Finally, our results underscore the growing need to focus on genotypes in biogeographical modelling and ecological forecasting.     

Range and niche shifts in response to past climate change in the desert horned lizard Phrynosoma platyrhinos

During climate change, species are often assumed to shift their geographic distributions (geographic ranges) in order to track environmental conditions – niches – to which they are adapted. Recent work, however, suggests that the niches do not always remain conserved during climate change but shift instead, allowing populations to persist in place or expand into new areas. We assessed the extent of range and niche shifts in response to the warming climate after the Last Glacial Maximum (LGM) in the desert horned lizard Phrynosoma platyrhinos, a species occupying the western deserts of North America. We used a phylogeographic approach with mitochondrial DNA sequences to approximate the species range during the LGM by identifying populations that exhibit a genetic signal of population stability versus those that exhibit a signal of a recent (likely post‐LGM) geographic expansion. We then compared the climatic niche that the species occupies today with the niche it occupied during the LGM using two models of simulated LGM climate. The genetic analyses indicated that P. platyrhinos persisted within the southern Mojave and Sonoran deserts throughout the latest glacial period and expanded from these deserts northwards, into the western and eastern Great Basin, after the LGM. The climatic niche comparisons revealed that P. platyrhinos expanded its climatic niche after the LGM towards novel, warmer and drier climates that allowed it to persist within the southern deserts. Simultaneously, the species shifted its climatic niche towards greater temperature and precipitation fluctuations after the LGM. We concluded that climatic changes at the end of the LGM promoted both range and niche shifts in this lizard. The mechanism that allowed the species to shift its niche remains unknown, but phenotypic plasticity likely contributes to the species ability to adjust to climate change.     

Niche differentiation in a postglacial colonizer,the bank vole Clethrionomys glareolus

Species‐level environmental niche modeling has been crucial in efforts to understand how species respond to climate variation and change. However, species often exhibit local adaptation and intraspecific niche differences that may be important to consider in predicting responses to climate. Here, we explore whether phylogeographic lineages of the bank vole originating from different glacial refugia (Carpathian, Western, Eastern, and Southern) show niche differentiation, which would suggest a role for local adaptation in biogeography of this widespread Eurasian small mammal. We first model the environmental requirements for the bank vole using species‐wide occurrences (210 filtered records) and then model each lineage separately to examine niche overlap and test for niche differentiation in geographic and environmental space. We then use the models to estimate past [Last Glacial Maximum (LGM) and mid‐Holocene] habitat suitability to compare with previously hypothesized glacial refugia for this species. Environmental niches are statistically significantly different from each other for all pairs of lineages in geographic and environmental space, and these differences cannot be explained by habitat availability within their respective ranges. Together with the inability of most of the lineages to correctly predict the distributions of other lineages, these results support intraspecific ecological differentiation in the bank vole. Model projections of habitat suitability during the LGM support glacial survival of the bank vole in the Mediterranean region and in central and western Europe. Niche differences between lineages and the resulting spatial segregation of habitat suitability suggest ecological differentiation has played a role in determining the present phylogeographic patterns in the bank vole. Our study illustrates that models pooling lineages within a species may obscure the potential for different responses to climate change among populations.     

GENETIC VARIATION IN THE PONDEROSAE OF THE SOUTHWEST

Ninety-five seedling populations of southwestern ponderosa pine (Pinus ponderosa var. scopulorum) along with single populations of Pinus engelmannii and Pinus arizonica were compared in four environmentally disparate common gardens. Differentiation among ponderosa pine populations was detected for a diverse assortment of variables that included patterns of shoot elongation, measures of growth potential, winter and spring freezing damage, and leaf characteristics. Multiple regression models accounted for as much as 85% of the variance among populations and described complex clines that were dominated by elevational and latitudinal effects. Although P. ponderosa, P. arizonica, and P. engelmannii were readily differentiated, the performance of progenies from one population suggested introgression primarily involving P. ponderosa and P. arizonica but also implicating P. engelmannii.     

Divergent lineages and conserved niches: using ecological niche modeling to examine the evolutionary patterns of the Nile monitor (<Emphasis Type="Italic">Varanus niloticus</Emphasis>)

Ecological niche modeling is a useful tool that can support phylogeographic analyses, offering insight into the evolutionary processes that have generated present-day patterns of biodiversity. Findings of ecological divergence across evolutionary lineages can be utilized to bolster inferences of parapatric or sympatric modes of speciation, and provide support for species-level classifications. Conversely, conserved ecological niches across evolutionary timescales are thought to have facilitated allopatric speciation. Here, we examined the climatic niche of three genetic lineages of the Nile monitor (Varanus niloticus) to better understand the processes involved in generating patterns of genetic variation, and to potentially clarify their taxonomic status. We built ecological niche models using genetically confirmed occurrence points from the three evolutionary lineages of V. niloticus, occupying the western, northern, and southern regions of Africa. Pairwise comparisons of climatic niche overlap provided evidence in support of niche conservatism across all V. niloticus lineages. These findings are consistent with an allopatric mode of differentiation. Furthermore, climatic niche conservatism could have played a role in isolating V. niloticus populations during historic climate oscillations, generating the observed genetic patterns across Africa.     

High genetic diversity and stable Pleistocene distributional ranges in the widespread Mexican red oak Quercus castanea Née (1801) (Fagaceae)

The Mexican highlands are areas of high biological complexity where taxa of Nearctic and Neotropical origin and different population histories are found. To gain a more detailed view of the evolution of the biota in these regions, it is necessary to evaluate the effects of historical tectonic and climate events on species. Here, we analyzed the phylogeographic structure, historical demographic processes, and the contemporary period, Last Glacial Maximum (LGM) and Last Interglacial (LIG) ecological niche models of Quercus castanea, to infer the historical population dynamics of this oak distributed in the Mexican highlands. A total of 36 populations of Q. castanea were genotyped with seven chloroplast microsatellite loci in four recognized biogeographic provinces of Mexico: the Sierra Madre Occidental (western mountain range), the Central Plateau, the Trans‐Mexican Volcanic Belt (TMVB, mountain range crossing central Mexico from west to east) and the Sierra Madre del Sur (SMS, southern mountain range). We obtained standard statistics of genetic diversity and structure and tested for signals of historical demographic expansions. A total of 90 haplotypes were identified, and 29 of these haplotypes were restricted to single populations. The within‐population genetic diversity was high (mean h_S = 0.72), and among‐population genetic differentiation showed a strong phylogeographic structure (N_ST = 0.630 > G_ST = 0.266; p < .001). Signals of demographic expansion were identified in the TMVB and the SMS. The ecological niche models suggested a considerable percentage of stable distribution area for the species during the LGM and connectivity between the TMVB and the SMS. High genetic diversity, strong phylogeographic structure, and ecological niche models suggest in situ permanence of Q. castanea populations with large effective population sizes. The complex geological and climatic histories of the TMVB help to explain the origin and maintenance of a large proportion of the genetic diversity in this oak species.     

EXPERIMENTAL STUDIES OF PONDEROSA PINE. III. DIFFERENCES IN PHOTOSYNTHESIS,STOMATAL CONDUCTANCE,AND WATER-USE EFFICIENCY BETWEEN TWO GENETIC LINES

As part of an intensive study of heritable differences among the progeny of Pinus ponderosa parents from two contrasting habitats (coastal vs. interior, continental), we examined the potential for differences in photosynthesis rate, stomatal conductance, and photosynthetic water-use efficiency. Plants from a cross between two coastal parents (ponderosa × ponderosa) exhibited lower photosynthetic water-use efficiencies, relative to plants from a coastal × interior cross (ponderosa × scopulorum). The lower water-use efficiencies in the ponderosa × ponderosa plants were evident as a lower ratio of external to intercellular CO₂ concentrations and higher stomatal conductances at any given rate of photosynthesis. The ponderosa × scopulorum plants exhibited lower stomatal conductances over a range of leaf-to-air water vapor concentration differences, which was partially explained by lower stomatal densities. The ponderosa × scopulorum plants also exhibited lower maximum photosynthesis rates and lower needle nitrogen concentrations. Taken together, the results suggest that in adapting to drier habitats, P. ponderosa has acquired improved water-use efficiencies and lower transpiration rates, but at the expense of reduced maximum photosynthesis rates.     

Phylogeography and genetic diversity of the widespread katydid Ducetia japonica (Thunberg, 1815) across China

Habitat fragmentation can lower migration rates and genetic connectivity among remaining populations of native species. Ducetia japonica is one of the most widespread katydids in China, but little is known about its genetic structure and phylogeographic distribution. We combined the five‐prime region of cytochrome c oxidase subunit I (COI‐5P), 11 newly developed microsatellite loci coupled with an ecological niche model (ENM) to examine the genetic diversity and population structure of D. japonica in China and beyond to Laos and Singapore. Both Bayesian inference (BI) and haplotype network methods revealed six mitochondrial COI‐5P lineages. The distribution of COI‐5P haplotypes may not demonstrate significant phylogeographic structure (N _ST > G _ST, p > .05). The STRUCTURE analysis based on microsatellite data also revealed six genetic clusters, but discordant with those obtained from COI‐5P haplotypes. For both COI‐5P and microsatellite data, Mantel tests revealed a significant positive correlation between geographic and genetic distances in mainland China. Bayesian skyline plot (BSP) analyses indicated that the population size of D. japonica''s three major mitochondrial COI‐5P lineages were seemingly not affected by last glacial maximum (LGM, 0.015–0.025 Mya). The ecological niche models showed that the current distribution of D. japonica was similar to the species’ distribution during the LGM period and only slightly extended in northern China. Further phylogeographic studies based on more extensive sampling are needed to identify specific locations of glacial refugia in northern China.     

Climate change and fire effects on a prairie–woodland ecotone: projecting species range shifts with a dynamic global vegetation model

Large shifts in species ranges have been predicted under future climate scenarios based primarily on niche‐based species distribution models. However, the mechanisms that would cause such shifts are uncertain. Natural and anthropogenic fires have shaped the distributions of many plant species, but their effects have seldom been included in future projections of species ranges. Here, we examine how the combination of climate and fire influence historical and future distributions of the ponderosa pine–prairie ecotone at the edge of the Black Hills in South Dakota, USA, as simulated by MC1, a dynamic global vegetation model that includes the effects of fire, climate, and atmospheric CO₂ concentration on vegetation dynamics. For this purpose, we parameterized MC1 for ponderosa pine in the Black Hills, designating the revised model as MC1‐WCNP. Results show that fire frequency, as affected by humidity and temperature, is central to the simulation of historical prairies in the warmer lowlands versus woodlands in the cooler, moister highlands. Based on three downscaled general circulation model climate projections for the 21st century, we simulate greater frequencies of natural fire throughout the area due to substantial warming and, for two of the climate projections, lower relative humidity. However, established ponderosa pine forests are relatively fire resistant, and areas that were initially wooded remained so over the 21st century for most of our future climate x fire management scenarios. This result contrasts with projections for ponderosa pine based on climatic niches, which suggest that its suitable habitat in the Black Hills will be greatly diminished by the middle of the 21st century. We hypothesize that the differences between the future predictions from these two approaches are due in part to the inclusion of fire effects in MC1, and we highlight the importance of accounting for fire as managed by humans in assessing both historical species distributions and future climate change effects.     

An Integrated Model of Environmental Effects on Growth,Carbohydrate Balance,and Mortality of Pinus ponderosa Forests in the Southern Rocky Mountains

Climate-induced tree mortality is an increasing concern for forest managers around the world. We used a coupled hydrologic and ecosystem carbon cycling model to assess temperature and precipitation impacts on productivity and survival of ponderosa pine (Pinus ponderosa). Model predictions were evaluated using observations of productivity and survival for three ponderosa pine stands located across an 800 m elevation gradient in the southern Rocky Mountains, USA, during a 10-year period that ended in a severe drought and extensive tree mortality at the lowest elevation site. We demonstrate the utility of a relatively simple representation of declines in non-structural carbohydrate (NSC) as an approach for estimating patterns of ponderosa pine vulnerability to drought and the likelihood of survival along an elevation gradient. We assess the sensitivity of simulated net primary production, NSC storage dynamics, and mortality to site climate and soil characteristics as well as uncertainty in the allocation of carbon to the NSC pool. For a fairly wide set of assumptions, the model estimates captured elevational gradients and temporal patterns in growth and biomass. Model results that best predict mortality risk also yield productivity, leaf area, and biomass estimates that are qualitatively consistent with observations across the sites. Using this constrained set of parameters, we found that productivity and likelihood of survival were equally dependent on elevation-driven variation in temperature and precipitation. Our results demonstrate the potential for a coupled hydrology-ecosystem carbon cycling model that includes a simple model of NSC dynamics to predict drought-related mortality. Given that increases in temperature and in the frequency and severity of drought are predicted for a broad range of ponderosa pine and other western North America conifer forest habitats, the model potentially has broad utility for assessing ecosystem vulnerabilities.     

EXPERIMENTAL STUDIES IN PONDEROSA PINE. I. RELATIONSHIP BETWEEN VARIATION IN PROTEINS AND MORPHOLOGY

Ponderosa pine from California (Pinus ponderosa var. ponderosa) were crossed to one another and also to individuals from the Rocky Mountains (P. p. var. scopulorum). All crosses involved a single mother and a single pollen donor. Patterns of inheritance of electrophoretically-detectable loci followed Mendelian expectations with one exception. Shikimate dehydrogenase showed unpredictable banding patterns in intervarietal crosses. Variability at these biochemical loci was compared to variability at 14 morphometric characters. The relationship between these two levels of variation is complex and permits only one generalization: variability at one level is not a good predictor of variability at the other level.     

Climate Warming Since the Holocene Accelerates West–East Communication for the Eurasian Temperate Water Strider Species Aquarius paludum

Holocene climate warming has dramatically altered biological diversity and distributions. Recent human-induced emissions of greenhouse gases will exacerbate global warming and thus induce threats to cold-adapted taxa. However, the impacts of this major climate change on transcontinental temperate species are still poorly understood. Here, we generated extensive genomic datasets for a water strider, Aquarius paludum, which was sampled across its entire distribution in Eurasia and used these datasets in combination with ecological niche modeling (ENM) to elucidate the influence of the Holocene and future climate warming on its population structure and demographic history. We found that A. paludum consisted of two phylogeographic lineages that diverged in the middle Pleistocene, which resulted in a “west–east component” genetic pattern that was probably triggered by Central Asia-Mongoxin aridification and Pleistocene glaciations. The diverged western and eastern lineages had a second contact in the Holocene, which shaped a temporary hybrid zone located at the boundary of the arid–semiarid regions of China. Future predictions detected a potentially novel northern corridor to connect the western and eastern populations, indicating west–east gene flow would possibly continue to intensify under future warming climate conditions. Further integrating phylogeographic and ENM analyses of multiple Eurasian temperate taxa based on published studies reinforced our findings on the “west–east component” genetic pattern and the predicted future northern corridor for A. paludum. Our study provided a detailed paradigm from a phylogeographic perspective of how transcontinental temperate species differ from cold-adapted taxa in their response to climate warming.     

Persistence and expansion of ponderosa pine woodlands in the west‐central Great Plains during the past two centuries

Aim Woody plant expansion and infilling in grasslands and savannas are occurring across a broad range of ecosystems around the globe and are commonly attributed to fire suppression, livestock grazing, nutrient enrichment and/or climate variability. In the western Great Plains, ponderosa pine (Pinus ponderosa) woodlands are expanding across broad geographical and environmental gradients. The objective of this study was to reconstruct the establishment of ponderosa pine in woodlands in the west‐central Great Plains and to identify whether it was mediated by climate variability. Location Our study took place in a 400‐km wide region from the base of the Front Range Mountains (c. 105° W) to the central Great Plains (c. 100° W) and from Nebraska (43° N) to northern New Mexico (36° N), USA. Methods Dates for establishment of ponderosa pine were reconstructed with tree rings in 11 woodland sites distributed across the longitudinal and latitudinal gradients of the study area. Temporal trends in decadal pine establishment were compared with summer Palmer Drought Severity Index (PDSI). Annual trends in pine establishment from 1985 to 2005 were compared with seasonal PDSI, temperature and moisture availability. Results Establishment of ponderosa pine occurred in the study area in all but one decade (1770s) between the 1750s and the early 2000s, with over 35% of establishment in the region occurring after 1980. Pine establishment was highly variable among sites. Across the region, decadal pine establishment was persistently low from 1940 to 1960, when PDSI was below average. Annual pine establishment from 1985 to 2005 was positively correlated with summer PDSI and inversely correlated with minimum spring temperatures. Main conclusions Most ponderosa pine woodlands pre‐date widespread Euro‐American settlement of the region around c. ad 1860 and currently have stable tree populations. High variability in the timing of establishment of pine among sites highlights the multiplicity of factors that can drive woodland dynamics, including land use, fire history, CO₂ enrichment, tree population dynamics and climate. Since the 1840s, the influence of climate was most notable across the study area during the mid‐20th century, when the establishment of pine was suppressed by two significant droughts. The past sensitivity of establishment of ponderosa pine to drought suggests that woodland expansion will be negatively affected by predicted increases in temperature and drought in the Great Plains.     

HISTORICAL SEPARATION AND PRESENT GENE FLOW THROUGH A ZONE OF SECONDARY CONTACT IN PONDEROSA PINE

I examined the effects of historical division and secondary contact between eastern and western varieties of ponderosa pine (Pinus ponderosa Laws Pinaceae) on extant patterns of genetic variation. Fossil and biogeographic evidence both indicate that the current point of contact between these two varieties represents secondary contact following historical separation during the Wisconsin glaciation. Current gene flow was assessed by observing the degree of introgression of paternally inherited cpDNA and maternally inherited mtDNA polymorphisms. Both seeds and pollen are wind dispersed in ponderosa pine. Introgression was primarily from west to east, the direction of the prevailing wind, for both organelles, but introgression of cpDNA far exceeded that of mtDNA. Thus pollen is the main agent of contemporary gene flow between the two varieties. Neither seeds nor pollen showed enough introgression since secondary contact to have homogenized the two gene pools. However, allozyme differentiation was minimal. This calls into question assumptions of selective neutrality for at least some of the markers. Theory predicts that nuclear markers will show a high locus-to-locus variance of F_ST following historical separation. This prediction is confirmed by the allozyme data for ponderosa pine, and may provide a useful means of identifying historical separations from allele frequency data.     

Genetic variation of piperidine alkaloids in Pinus ponderosa: a common garden study

Background and Aims

Previous measurements of conifer alkaloids have revealed significant variation attributable to many sources, environmental and genetic. The present study takes a complementary and intensive, common garden approach to examine genetic variation in Pinus ponderosa var. ponderosa alkaloid production. Additionally, this study investigates the potential trade-off between seedling growth and alkaloid production, and associations between topographic/climatic variables and alkaloid production.

Methods

Piperidine alkaloids were quantified in foliage of 501 nursery seedlings grown from seed sources in west-central Washington, Oregon and California, roughly covering the western half of the native range of ponderosa pine. A nested mixed model was used to test differences among broad-scale regions and among families within regions. Alkaloid concentrations were regressed on seedling growth measurements to test metabolite allocation theory. Likewise, climate characteristics at the seed sources were also considered as explanatory variables.

Key Results

Quantitative variation from seedling to seedling was high, and regional variation exceeded variation among families. Regions along the western margin of the species range exhibited the highest alkaloid concentrations, while those further east had relatively low alkaloid levels. Qualitative variation in alkaloid profiles was low. All measures of seedling growth related negatively to alkaloid concentrations on a natural log scale; however, coefficients of determination were low. At best, annual height increment explained 19·4 % of the variation in ln(total alkaloids). Among the climate variables, temperature range showed a negative, linear association that explained 41·8 % of the variation.

Conclusions

Given the wide geographic scope of the seed sources and the uniformity of resources in the seedlings'' environment, observed differences in alkaloid concentrations are evidence for genetic regulation of alkaloid secondary metabolism in ponderosa pine. The theoretical trade-off with seedling growth appeared to be real, however slight. The climate variables provided little evidence for adaptive alkaloid variation, especially within regions.Key words: Pinus ponderosa var. ponderosa, Pinaceae, 2,6-disubstituted piperidine alkaloids, secondary products, geographic variation, progeny study, plant defense, Growth–Differentiation Balance Hypothesis, PRISM     

Long-Distance Dispersal after the Last Glacial Maximum (LGM) Led to the Disjunctive Distribution of Pedicularis kansuensis (Orobanchaceae) between the Qinghai-Tibetan Plateau and Tianshan Region

Quaternary climate fluctuations have profoundly affected the current distribution patterns and genetic structures of many plant and animal species in the Qinghai-Tibetan Plateau (QTP) and adjacent mountain ranges, e.g. Tianshan (TSR), Altay, etc. In this greater area disjunct distributions are prominent but have nevertheless received little attention with respect to the historical processes involved. Here, we focus on Pedicularis kansuensis to test whether the current QTP and TSR disjunction is the result of a recent Holocene range expansion involving dispersal across arid land bridge(s) or a Pleistocene range fragmentation involving persistence in refugia. Two chloroplast DNA spacers were sequenced for 319 individuals from 34 populations covering the entire distribution range of this species in China. We found a total of 17 haplotypes of which all occurred in the QTP, and only five in the TSR. Overall genetic diversity was high (H_T = 0.882, H_S = 0.559) and higher in the QTP than in the TSR. Genetic differentiation among regions and populations was relatively low (G_ST = 0.366) and little evidence for a phylogeographic pattern emerged. The divergence times for the four main lineages could be dated to the early Pleistocene. Surprisingly, the two ubiquitous haplotypes diverged just before or around the Last Glacial Maximum (LGM) and were found in different phylogenetic lineages. The Species Distribution Model suggested a disappearance of P. kansuensis from the TSR during the LGM in contrast to a relatively constant potential distribution in the QTP. We conclude that P. kansuensis colonized the TSR after the LGM. The improbable long-distance dispersal by wind or water across arid land seed flow may well have had birds or men as vector.     

Pleistocene Niche Stability and Lineage Diversification in the Subtropical Spider Araneus omnicolor (Araneidae)

The influence of Quaternary climate oscillations on the diversification of the South American fauna is being increasingly explored. However, most of these studies have focused on taxa that are endemic to tropical environments, and relatively few have treated organisms restricted to subtropical biomes. Here we used an integrative phylogeographical framework to investigate the effects of these climate events on the ecological niche and genetic patterns of the subtropical orb-weaver spider Araneus omnicolor (Araneidae). We analyzed the mitochondrial (Cytochrome Oxidase I, COI) and nuclear (Internal Transcribed Subunit II, ITS2) DNA of 130 individuals throughout the species’ range, and generated distribution models in three different climate scenarios [present, Last Glacial Maximum (LGM), and Last Interglacial Maximum (LIG)]. Additionally, we used an Approximate Bayesian Computation (ABC) approach to compare possible demographic scenarios and select the hypothesis that better explains the genetic patterns of A. omnicolor. We obtained high haplotype diversity but low nucleotide variation among sequences. The population structure and demographic analyses showed discrepancies between markers, suggesting male-biased dispersal in the species. The time-calibrated COI phylogenetic inference showed a recent diversification of lineages (Middle/Late Pleistocene), while the paleoclimate modeling indicated niche stability since ~120 Kya. The ABC results agreed with the niche models, supporting a panmictic population as the most likely historical scenario for the species. These results indicate that A. omnicolor experienced no niche or population reductions during the Late Pleistocene, despite the intense landscape modifications that occurred in the subtropical region, and that other factors beside LGM and LIG climate oscillations might have contributed to the demographic history of this species. This pattern may be related to the high dispersal ability and wide environmental tolerance of A. omnicolor, highlighting the need for more phylogeographical studies with invertebrates and other generalist taxa, in order to understand the effects of Quaternary climate changes on Neotropical biodiversity.     

Primers designed to amplify a mitochondrial nad1 intron in ponderosa pine, Pinus ponderosa, limber pine, P. flexilis, and Scots pine, P. sylvestris

The b/c intron of the mitochondrial nad1 gene, was sequenced to characterize the indel region of ponderosa pine, Pinus ponderosa. The sequence in ponderosa pine was aligned with the sequence in Scots pine, Pinus sylvestris, to design seven primers that are useful for sequencing and for revealing size variation in amplified fragments in ponderosa pine, Scots pine, and limber pine, Pinus flexilis. These primers reveal variability in all three species, and the pattern of variability within ponderosa pine is described by a preliminary survey. The indel region of ponderosa pine contains three distinct elements with lengths of 31, 32, and 34 bp. Received: 1 March 2000 / Accepted: 14 April 2000<@head-com-p1a.lf>Communicated by P.M.A. Tigerstedt     

A phyloclimatic study of Cyclamen

Background

The impact of global climate change on plant distribution, speciation and extinction is of current concern. Examining species climatic preferences via bioclimatic niche modelling is a key tool to study this impact. There is an established link between bioclimatic niche models and phylogenetic diversification. A next step is to examine future distribution predictions from a phylogenetic perspective. We present such a study using Cyclamen (Myrsinaceae), a group which demonstrates morphological and phenological adaptations to its seasonal Mediterranean-type climate. How will the predicted climate change affect future distribution of this popular genus of garden plants?

Results

We demonstrate phylogenetic structure for some climatic characteristics, and show that most Cyclamen have distinct climatic niches, with the exception of several wide-ranging, geographically expansive, species. We reconstruct climate preferences for hypothetical ancestral Cyclamen. The ancestral Cyclamen lineage has a preference for the seasonal Mediterranean climate characteristic of dry summers and wet winters. Future bioclimatic niches, based on BIOCLIM and Maxent models, are examined with reference to a future climate scenario for the 2050s. Over the next 50 years we predict a northward shift in the area of climatic suitability, with many areas of current distribution becoming climatically unsuitable. The area of climatic suitability for every Cyclamen species is predicted to decrease. For many species, there may be no areas with a suitable climate regardless of dispersal ability, these species are considered to be at high risk of extinction. This risk is examined from a phylogenetic perspective.

Conclusion

Examining bioclimatic niches from a phylogenetic perspective permits novel interpretations of these models. In particular, reconstruction of ancestral niches can provide testable hypothesis about the historical development of lineages. In the future we can expect a northwards shift in climatic suitability for the genus Cyclamen. If this proves to be the case then dispersal is the best chance of survival, which seems highly unlikely for ant-dispersed Cyclamen. Human-assisted establishment of Cyclamen species well outside their native ranges offers hope and could provide the only means of dispersal to potentially suitable future environments. Even without human intervention the phylogenetic perspective demonstrates that major lineages could survive climate change even if many species are lost.     

Phylogeography and ecological niche modelling of the New Zealand stick insect Clitarchus hookeri (White) support survival in multiple coastal refugia

Aim Increasing our understanding of the effects of the Last Glacial Maximum (LGM) and determining the location of refugia requires studies on widely distributed species with dense sampling of populations. We have reconstructed the biogeographic history of Clitarchus hookeri (White), a widespread species of New Zealand stick insect that exhibits geographic parthenogenesis, using phylogeographic analysis and ecological niche modelling. Location New Zealand. Methods We used DNA sequence data from the mitochondrial cytochrome c oxidase subunit I gene to reconstruct phylogenetic relationships among haplotypes from C. hookeri and two undescribed Clitarchus species. We also used distribution data from our own field surveys and museum records to reconstruct the geographic distribution of C. hookeri during the present and the LGM, using ecological niche modelling. Results The ecological niche models showed that the geographic distribution of C. hookeri has expanded dramatically since the LGM. Our model predicted large areas of suitable LGM habitat in upper North Island, and small patches along the east coast of South Island. The phylogeographic analysis shows that populations in the northern half of North Island contain much higher levels of genetic variation than those from southern North Island and South Island, and is congruent with the ecological niche model. The distribution of bisexual populations is also non-random, with males completely absent from South Island and very rare in southern North Island. Main conclusions During the LGM C. hookeri was most likely restricted to several refugia in upper North Island and one or more smaller refugia along the east coast of South Island. The unisexual populations predominate in post-glacial landscapes and are clearly favoured in the recolonization of such areas. Our study exemplifies the utility of integrating ecological niche modelling and phylogeographic analysis.