Vegetation cover of Brazil in the last 21 ka: New insights into the Amazonian refugia and Pleistocenic arc hypotheses

Aim

The two main hypotheses about the Neotropical palaeovegetation, namely that of Amazonian refugia by Haffer and of the Pleistocene arc by Prado and Gibbs, are still constantly debated. We offer new insights on this debate using ecological niche modelling with combined climate–soil predictors to test both hypotheses, reconstruct the palaeovegetation of the Last Glacial Maximum (LGM; 21 ka) and Mid‐Holocene (Mid‐H; 6 ka) and indicate the configuration of refugia areas.

Location

Brazil.

Time period

Last 21 ka.

Major taxa studied

Biomes.

Methods

We modelled the environmental space of the 10 most representative biomes with the RandomForest classifier, using climate predictors from three atmospheric general circulation models (CCSM4, MPI‐ESM‐P and MIROC‐ESM) and soil predictors, the same for the different situations. Based on the consensus among the models, we reconstructed the palaeovegetation cover for LGM and Mid‐H and used fossil pollen sites to validate the reconstructions in a direct comparison.

Results

The climate in the past was cooler and wetter throughout most of the territory. The Amazon basin region was the most affected by climate change in the last 21 ka, with equatorial rain forest retracting to refugia areas, while the tropical rain forest (with climatic preferences similar to the Atlantic forest) expanded in the basin. In southern Brazil, the mixed forest (Araucaria forest) shifted to lower latitudes, while the grasslands expanded. In most biomes, the greatest changes occurred in the ecotonal zones, supported by pollen fossils.

Main conclusions

With regard to Haffer's hypothesis, the forests of the Amazonian lowlands retreated to refugia areas, while the colder and wetter climate of the basin created a favourable niche for another type of forest, instead of savanna. The advance of dry vegetation was restricted to ecotonal conditions, preventing the formation of a continuous Pleistocene arc, predicted by Prado and Gibbs's hypothesis.     

Ice‐age persistence and genetic isolation of the disjunct distribution of larch in Alaska

Larix laricina (eastern larch, tamarack) is a transcontinental North American conifer with a prominent disjunction in the Yukon isolating the Alaskan distribution from the rest of its range. We investigate whether in situ persistence during the last glacial maximum (LGM) or long‐distance postglacial migration from south of the ice sheets resulted in the modern‐day Alaskan distribution. We analyzed variation in three chloroplast DNA regions of 840 trees from a total of 69 populations (24 new sampling sites situated on both sides of the Yukon range disjunction pooled with 45 populations from a published source) and conducted ensemble species distribution modeling (SDM) throughout Canada and United States to hindcast the potential range of L. laricina during the LGM. We uncovered the genetic signature of a long‐term isolation of larch populations in Alaska, identifying three endemic chlorotypes and low levels of genetic diversity. Range‐wide analysis across North America revealed the presence of a distinct Alaskan lineage. Postglacial gene flow across the Yukon divide was unidirectional, from Alaska toward previously glaciated Canadian regions, and with no evidence of immigration into Alaska. Hindcast SDM indicates one of the broadest areas of past climate suitability for L. laricina existed in central Alaska, suggesting possible in situ persistence of larch in Alaska during the LGM. Our results provide the first unambiguous evidence for the long‐term isolation of L. laricina in Alaska that extends beyond the last glacial period and into the present interglacial period. The lack of gene flow into Alaska along with the overall probability of larch occurrence in Alaska being currently lower than during the LGM suggests that modern‐day Alaskan larch populations are isolated climate relicts of broader glacial distributions, and so are particularly vulnerable to current warming trends.     

Quaternary climate instability is correlated with patterns of population genetic variability in Bombus huntii

Climate oscillations have left a significant impact on the patterns of genetic diversity observed in numerous taxa. In this study, we examine the effect of Quaternary climate instability on population genetic variability of a bumble bee pollinator species, Bombus huntii in western North America. Pleistocene and contemporary B. huntii habitat suitability (HS) was estimated with an environmental niche model (ENM) by associating 1,035 locality records with 10 bioclimatic variables. To estimate genetic variability, we genotyped 380 individuals from 33 localities at 13 microsatellite loci. Bayesian inference was used to examine population structure with and without a priori specification of geographic locality. We compared isolation by distance (IBD) and isolation by resistance (IBR) models to examine population differentiation within and among the Bayesian inferred genetic clusters. Furthermore, we tested for the effect of environmental niche stability (ENS) on population genetic diversity with linear regression. As predicted, high‐latitude B. huntii habitats exhibit low ENS when compared to low‐latitude habitats. Two major genetic clusters of B. huntii inhabit western North America: (a) a north genetic cluster predominantly distributed north of 28°N and (b) a south genetic cluster distributed south of 28°N. In the south genetic cluser, both IBD and IBR models are significant. However, in the north genetic cluster, IBD is significant but not IBR. Furthermore, the IBR models suggest that low‐latitude montane populations are surrounded by habitat with low HS, possibly limiting dispersal, and ultimately gene flow between populations. Finally, we detected high genetic diversity across populations in regions that have been climatically unstable since the last glacial maximum (LGM), and low genetic diversity across populations in regions that have been climatically stable since the LGM. Understanding how species have responded to climate change has the potential to inform management and conservation decisions of both ecological and economic concerns.     

River islands,refugia and genetic structuring in the endemic brown frog Rana kukunoris (Anura,Ranidae) of the Qinghai‐Tibetan Plateau

Frequently, Pleistocene climatic cycling has been found to be the diver of genetic structuring in populations, even in areas that did not have continental ice sheets, such as on the Qinghai‐Tibetan Plateau (QTP). Typically, species distributed on the plateau have been hypothesized to re‐treat to south‐eastern refugia, especially during the Last Glacial Maximum (LGM). We evaluated sequence variation in the mitochondrial DNA gene Cytb and the nuclear DNA gene RAG‐1 in Rana kukunoris, a species endemic to the QTP. Two major lineages, N and S, were identified, and lineage N was further subdivided into N1 and N2. The geographical distribution and genealogical divergences supported the hypothesis of multiple refugia. However, major lineages and sublineages diverged prior to the LGM. Demographical expansion was detected only in lineage S and sublineage N2. Sublineage N1 might have survived several glacial cycles in situ and did not expand after the LGM because of the absence of suitable habitat; it survived in river islands. Genetic analysis and environment modelling suggested that the north‐eastern edge of QTP contained a major refugium for R. kukunoris. From here, lineage S dispersed southwards after the LGM. Two microrefugia in northern Qilian Mountains greatly contributed to current level of intraspecific genetic diversity. These results were found to have important implications for the habitat conservation in Northwest China.     

Phylogeography of the world's tallest angiosperm, Eucalyptus regnans: evidence for multiple isolated Quaternary refugia

Aim There is a need for more Southern Hemisphere phylogeography studies, particularly in Australia, where, unlike much of Europe and North America, ice sheet cover was not extensive during the Last Glacial Maximum (LGM). This study examines the phylogeography of the south‐east Australian montane tree species Eucalyptus regnans. The work aimed to identify any major evolutionary divergences or disjunctions across the species’ range and to examine genetic signatures of past range contraction and expansion events. Location South‐eastern mainland Australia and the large island of Tasmania. Methods We determined the chloroplast DNA haplotypes of 410 E. regnans individuals (41 locations) based on five chloroplast microsatellites. Genetic structure was examined using analysis of molecular variance (AMOVA), and a statistical parsimony tree was constructed showing the number of nucleotide differences between haplotypes. Geographic structure in population genetic diversity was examined with the calculation of diversity parameters for the mainland and Tasmania, and for 10 regions. Regional analysis was conducted to test hypotheses that some areas within the species’ current distribution were refugia during the LGM and that other areas have been recolonized by E. regnans since the LGM. Results Among the 410 E. regnans individuals analysed, 31 haplotypes were identified. The statistical parsimony tree shows that haplotypes divided into two distinct groups corresponding to mainland Australia and Tasmania. The distribution of haplotypes across the range of E. regnans shows strong geographic patterns, with many populations and even certain regions in which a particular haplotype is fixed. Many locations had unique haplotypes, particularly those in East Gippsland in south‐eastern mainland Australia, north‐eastern Tasmania and south‐eastern Tasmania. Higher haplotype diversity was found in putative refugia, and lower haplotype diversity in areas likely to have been recolonized since the LGM. Main conclusions The data are consistent with the long‐term persistence of E. regnans in many regions and the recent recolonization of other regions, such as the Central Highlands of south‐eastern mainland Australia. This suggests that, in spite of the narrow ecological tolerances of the species and the harsh environmental conditions during the LGM, E. regnans was able to persist locally or contracted to many near‐coastal refugia, maintaining a diverse genetic structure.     

Genetic diversity and ecological niche modelling of the restricted Recordia reitzii (Verbenaceae) from southern Brazilian Atlantic forest

Genetic diversity analyses, coupled with ecological niche modelling (ENM) of species with a restricted distribution, may provide valuable information for understanding diversification patterns in endangered areas. We analyzed the genetic diversity of Recordia reitzii, a tree restricted to the threatened and highly fragmented Brazilian Atlantic forest, using three intergenic cpDNA spacers and ten microsatellite (SSR) loci. To assess the historical processes that may have influenced the distribution of extant R. reitzii populations, the current potential distributions of R. reitzii and Recordia boliviana, a closely related species, were modelled and projected onto the Last Glacial Maximum (LGM) and Last Interglacial (LIG) periods. Niche divergence was quantified between these two. The cpDNA and SSR data showed a north–south pattern of the diversity distribution and structured populations, suggesting that gene flow is probably limited. According to our data, R. reitzii exhibits low genetic diversity, which may be a result of a founder or distribution‐reduction effect, narrow distribution or small population size. The ecological niche models showed a wider palaeodistribution during the LIG and a retraction during the LGM for both species. Tests of niche divergence and conservatism indicated that bioclimatic factors might have influenced the diversification of these Recordia species. © 2014 The Linnean Society of London, Botanical Journal of the Linnean Society, 2014, 176 , 332–348.     

Identification of glacial refugia in south-eastern North America by phylogeographical analyses of a forest understorey plant, Trillium cuneatum

Aim We examine several hypotheses emerging from biogeographical and fossil records regarding glacial refugia of a southern thermophilic plant species. Specifically, we investigated the glacial history and post‐glacial colonization of a forest understorey species, Trillium cuneatum. We focused on the following questions: (1) Did T. cuneatum survive the Last Glacial Maximum (LGM) in multiple refugia, and (if so) where were they located, and is the modern genetic structure congruent with the fossil record‐based reconstruction of refugia for mesic deciduous forests? (2) What are the post‐glacial colonization patterns in the present geographical range? Location South‐eastern North America. Methods We sampled 45 populations of T. cuneatum throughout its current range. We conducted phylogeographical analyses based on maternally inherited chloroplast DNA (cpDNA haplotypes) and used TCS software to reconstruct intraspecific phylogeny. Results We detected six cpDNA haplotypes, geographically highly structured into non‐overlapping areas. With one exception, none of the populations had mixed haplotype composition. TCS analysis resulted in two intraspecific cpDNA lineages, with one clade subdivided further by shallower diversification. Main conclusions Our investigation revealed that T. cuneatum survived the LGM in multiple refugia, belonging to two (western, eastern) genealogical lineages geographically structured across south‐eastern North America. The western clade is confined to the south‐western corner of T. cuneatum’s modern range along the Lower Mississippi Valley, where fossil records document a major refugium of mesic deciduous forest. For the eastern clade, modern patterns of cpDNA haplotype distribution suggest cryptic vicariance, in the form of forest contractions and subsequent expansions associated with Pleistocene glacial cycles, rather than simple southern survival and subsequent northward colonization. The north–south partitioning of cpDNA haplotypes was unexpected, suggesting that populations of this rather southern thermophilic species may have survived in more northern locations than initially expected based on LGM climate reconstruction, and that the Appalachian Mountains functioned as a barrier to the dispersal of propagules originating in more southern refugia. Furthermore, our results reveal south‐west to north‐east directionality in historical migration through the Valley and Ridge region of north‐west Georgia.     

Ancient DNA supports southern survival of Richardson's collared lemming (Dicrostonyx richardsoni) during the last glacial maximum

Collared lemmings (genus Dicrostonyx) are circumpolar Arctic arvicoline rodents associated with tundra. However, during the last glacial maximum (LGM), Dicrostonyx lived along the southern ice margin of the Laurentide ice sheet in communities comprising both temperate and boreal species. To better understand these communities and the fate of these southern individuals, we compare mitochondrial cytochrome b sequence data from three LGM‐age Dicrostonyx fossils from south of the Laurentide ice sheet to sequences from modern Dicrostonyx sampled from across their present‐day range. We test whether the Dicrostonyx populations from LGM‐age continental USA became extinct at the Pleistocene–Holocene transition ~11000 years ago or, alternatively, if they belong to an extant species whose habitat preferences can be used to infer the palaeoclimate along the glacial margin. Our results indicate that LGM‐age Dicrostonyx from Iowa and South Dakota belong to Dicrostonyx richardsoni, which currently lives in a temperate tundra environment west of Hudson Bay, Canada. This suggests a palaeoclimate south of the Laurentide ice sheet that contains elements similar to the more temperate shrub tundra characteristic of extant D. richardsoni habitat, rather than the very cold, dry tundra of the Northern Arctic. While more data are required to determine whether or not the LGM southern population is ancestral to extant D. richardsoni, it seems most probable that the species survived the LGM in a southern refugium.     

The impact of early Quaternary climate change on the diversification and population dynamics of a South American cactus species

Aim

Climatic oscillations have been suggested to promote speciation and changes in species distributions, mostly in connection with the Last Glacial Maximum (LGM). However, the LGM is just the most recent of the 20+ glacial‐interglacial periods that characterise the Quaternary. Here, we investigate the role of climatic changes and geomorphological features in shaping the evolution, distribution and population dynamics of the South American cactus Cereus hildmannianus.

Location

South‐eastern South America.

Methods

We built a large fossil‐calibrated phylogeny for cacti (family Cactaceae), comprising 128 species distributed in all subfamilies, using a Bayesian relaxed clock. We used the results to derive a secondary calibration for a population‐level phylogeny in C. hildmannianus. We amplified two plastid (trnQ‐5′rps16 and psbJ‐petA) and one nuclear marker (PhyC) for 24 populations. We estimated population dynamics, ancestral areas, and species distribution models to infer the clade's evolutionary history in time and space.

Results

Our results show a major population divergence of C. hildmannianus at c. 2.60 Ma, which is strikingly coincident with the transition of the Pliocene–Pleistocene and onset of Quaternary glaciations. This was followed by a complex phylogeographic scenario involving population expansions across ecologically diverse regions.

Main conclusions

Contrary to the dominant research focus on the LGM, our study indicates a major impact of the first Quaternary glaciation on the distribution and population divergence of a South American plant species. Further intraspecific events seem related to successive climatic changes and geomorphology, including the development of the coastal plain and its peculiar diversity. We propose that the first Quaternary glaciation acted as a major evolutionary bottleneck, whereby many warm‐adapted lineages succumbed, while those that survived could diversify and better cope with subsequent climatic oscillations.     

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.     

Pleistocene climatic fluctuations drive isolation and secondary contact in the red diamond rattlesnake (Crotalus ruber) in Baja California

Aim

Many studies have investigated the phylogeographic history of species on the Baja California Peninsula, and they often show one or more genetic breaks that are spatially concordant among many taxa. These phylogeographic breaks are commonly attributed to vicariance as a result of geological or climatic changes, followed by secondary contact when barriers are no longer present. We use restriction‐site associated DNA sequence data and a phylogeographic model selection approach to explicitly test the secondary contact hypothesis in the red diamond rattlesnake, Crotalus ruber.

Location

Baja California and Southern California.

Methods

We used phylogenetic and population clustering approaches to identify population structure. We then used coalescent methods to simultaneously estimate population parameters and test the fit of phylogeographic models to the data. We used ecological niche models to infer suitable habitat for C. ruber at the Last Glacial Maximum (LGM).

Results

Crotalus ruber is composed of distinct northern and southern populations with a boundary near the town of Loreto in Baja California Sur. A model of isolation followed by secondary contact provides the best fit to the data, with both divergence and contact occurring in the Pleistocene. We also identify a genomic signature of northern range expansion in the northern population, consistent with LGM niche models showing that the northern‐most portion of the range of C. ruber was not suitable habitat during the LGM.

Main conclusions

We provide the first explicitly model‐based test of the secondary contact model in Baja California and show that populations of C. ruber were isolated before coming back into contact near Loreto, a region that shows phylogeographic breaks for other taxa. Given the timing of divergence and contact, we suggest that climatic fluctuations have driven the observed phylogeographic structure observed in C. ruber and that they may have driven similar patterns in other taxa.     

Scattered late‐glacial and early Holocene tree populations as dispersal nuclei for forest development in north‐eastern European Russia

Aim Concepts about patterns and rates of post‐glacial tree population migration are changing as a result of the increasing amount of palaeobotanical information being provided by macroscopic plant remains. Here we combine macrofossil, pollen and stomata records from five sites in north‐eastern European Russia and summarize the results for the late‐glacial–early Holocene transition. The late‐glacial–early Holocene transition encompasses the first indications of trees (tree‐type Betula, Picea abies, Abies sibirica and Larix sibirica) and subsequent forest development. Considerable time‐lags between the first macrobotanical and/or stomata finds of spruce (Picea abies) and the establishment of a closed forest are reconsidered. Location Pechora basin, north‐eastern European Russia. Methods We used plant macrofossil, stomata, pollen and radiocarbon analyses to reconstruct late‐glacial and early Holocene tree establishment and forest development. The data were derived from lake sediment and peat archives. Results Palaeobotanical data reveal an early Holocene presence (11,500–10,000 cal. yr bp ) of arboreal taxa at all five sites. One site presently located in the northernmost taiga zone, shows the presence of spruce and reproducing tree birch during the late‐glacial. Given the current view of post‐glacial population dynamics and migration rates, it seems likely that the source area of these early tree populations in north‐eastern European Russia was not located in southern Europe but that these populations had local origins. Results thus support the emerging view that the first post‐glacial population expansions in non‐glaciated regions at high latitudes do not reflect migration from the south but were a result of an increase in the size and density of small persisting outlying tree populations. Main conclusions Results suggest that the area east of the margin of the Scandinavian ice sheet to the Ural Mountains had isolated patches of trees during the late‐glacial and early Holocene and that these small populations acted as initial nuclei for population expansion and forest development in the early Holocene.     

Impact of Pleistocene aridity oscillations on the population history of a widespread,vagile Australian mammal,Macropus fuliginosus

Aim Climatic fluctuations during the Pleistocene have shaped the population structure of many extant taxa. However, few studies have examined widespread species inhabiting the Australian continent, where periods of increased aridity characterized the Pleistocene. Here we investigate the phylogeography and population history of a widespread and vagile southern Australian marsupial, the western grey kangaroo (Macropus fuliginosus). Location Southern Australia. Methods We examined the variation of the mitochondrial DNA (mtDNA) control region from 511 individuals of M. fuliginosus sampled throughout their transcontinental distribution. Maximum likelihood and Bayesian analyses were used to investigate the phylogeography and coalescence analyses were then used to test hypothesized biogeographical scenarios. Results The combined results of the phylogeographical and coalescence analyses revealed a complex evolutionary history. Macropus fuliginosus originated in the south‐west of the continent, with north‐western and south‐western populations subsequently diverging as a result of vicariance events during the mid‐Pleistocene. Subsequent arid phases affected these populations differently. In the north‐west, the expansion and contraction of the arid zone resulted in repeated vicariance events and multiple divergent north‐western mtDNA subclades. In contrast, the south‐western population was less impacted by climatic oscillations but gave rise to a major transcontinental eastward expansion. Main conclusions Macropus fuliginosus exhibits the genetic signature of divergence due to unidentified barriers in south‐western Western Australia, while previously identified barriers across southern Australia appear to have had little impact despite evidence of a broad‐scale range expansion prior to the Last Glacial Maximum (LGM). This pattern of localized expansion and contraction is comparable to unglaciated regions in both the Northern and Southern Hemispheres. Furthermore, this study indicates that despite the potential similarities between Northern Hemisphere glaciation and the activation of dune systems in the Australian arid zone, both of which rendered large areas inhospitable, the biotic responses and resultant phylogeographical signatures are dissimilar. Whereas a limited number of major geographically concordant refugia are observed in glaciated areas, the Southern Hemisphere arid zone appears to be associated with multiple species‐specific idiosyncratic refugia.     

A complex pattern of post‐divergence expansion,contraction, introgression,and asynchronous responses to Pleistocene climate changes in two Dipelta sister species from western China

The well‐known vicariance and dispersal models dominate in understanding the allopatric pattern for related species and presume the simultaneous occurrence of speciation and biogeographic events. However, the formation of allopatry could postdate the species divergence. We examined this hypothesis using DNA sequence data from three chloroplast fragments and five nuclear loci of Dipelta floribunda Maxim. and D. yunnanensis Franch, two shrub species with the circum Sichuan Basin distribution, combining the climatic niche modeling approach. The best‐fit model supported by the approximate Bayesian computation analysis indicated that D. floribunda and D. yunnanensis diverged during the mid‐Pleistocene period, consistent with the largest glacial period in the Qinghai–Tibet Plateau. The historically interspecific gene flow was identified, but seemed to have ceased after the last interglacial period, when the range of D. floribunda moved northward from the south of the Sichuan Basin. Furthermore, populations of D. floribunda had expanded obviously in the north of the Sichuan Basin after the last glacial maximum (LGM). Relatively, the range of D. yunnanensis expanded before the LGM, and reduced during the post‐LGM especially in the north of the Sichuan Basin, reflecting the asynchronous responses of related species to contemporary climate changes. Our results suggested that complex topography should be considered in understanding distributional patterns, even for closely related species and their demographic responses.     

Pollen-based reconstructions of biome distributions for Australia, Southeast Asia and the Pacific (SEAPAC region) at 0, 6000 and 18,000 14C yr BP

Aim This paper documents reconstructions of the vegetation patterns in Australia, Southeast Asia and the Pacific (SEAPAC region) in the mid‐Holocene and at the last glacial maximum (LGM). Methods Vegetation patterns were reconstructed from pollen data using an objective biomization scheme based on plant functional types. The biomization scheme was first tested using 535 modern pollen samples from 377 sites, and then applied unchanged to fossil pollen samples dating to 6000 ± 500 or 18,000 ± 1000 ¹⁴C yr bp . Results 1. Tests using surface pollen sample sites showed that the biomization scheme is capable of reproducing the modern broad‐scale patterns of vegetation distribution. The north–south gradient in temperature, reflected in transitions from cool evergreen needleleaf forest in the extreme south through temperate rain forest or wet sclerophyll forest (WSFW) and into tropical forests, is well reconstructed. The transitions from xerophytic through sclerophyll woodlands and open forests to closed‐canopy forests, which reflect the gradient in plant available moisture from the continental interior towards the coast, are reconstructed with less geographical precision but nevertheless the broad‐scale pattern emerges. 2. Differences between the modern and mid‐Holocene vegetation patterns in mainland Australia are comparatively small and reflect changes in moisture availability rather than temperature. In south‐eastern Australia some sites show a shift towards more moisture‐stressed vegetation in the mid‐Holocene with xerophytic woods/scrub and temperate sclerophyll woodland and shrubland at sites characterized today by WSFW or warm‐temperate rain forest (WTRF). However, sites in the Snowy Mountains, on the Southern Tablelands and east of the Great Dividing Range have more moisture‐demanding vegetation in the mid‐Holocene than today. South‐western Australia was slightly drier than today. The single site in north‐western Australia also shows conditions drier than today in the mid‐Holocene. Changes in the tropics are also comparatively small, but the presence of WTRF and tropical deciduous broadleaf forest and woodland in the mid‐Holocene, in sites occupied today by cool‐temperate rain forest, indicate warmer conditions. 3. Expansion of xerophytic vegetation in the south and tropical deciduous broadleaf forest and woodland in the north indicate drier conditions across mainland Australia at the LGM. None of these changes are informative about the degree of cooling. However the evidence from the tropics, showing lowering of the treeline and forest belts, indicates that conditions were between 1 and 9 °C (depending on elevation) colder. The encroachment of tropical deciduous broadleaf forest and woodland into lowland evergreen broadleaf forest implies greater aridity. Main conclusions This study provides the first continental‐scale reconstruction of mid‐Holocene and LGM vegetation patterns from Australia, Southeast Asia and the Pacific (SEAPAC region) using an objective biomization scheme. These data will provide a benchmark for evaluation of palaeoclimate simulations within the framework of the Palaeoclimate Modelling Intercomparison Project.     

Interglacial refugia on tropical mountains: Novel insights from the summit rat (Rattus baluensis), a Borneo mountain endemic

Aim

The genetics of organisms currently isolated in refugia has received little attention compared to post‐glacial expansions. We study the population history and connectivity of a rat endemic to montane habitat in Borneo to better understand the history and potential of populations in interglacial mountain refugia.

Location

Sabah, Borneo, Malaysia.

Methods

We performed a field survey of the summit rat (Rattus baluensis) on two mountains, Mt. Kinabalu and Mt. Tambuyukon, its entire known distribution. We sequenced mitogenomes and 27 introns (19 of which were polymorphic) in 49 individuals from both populations. We analysed their current genetic structure and diversity, and inferred their demographic history with approximate Bayesian computation.

Results

Summit rats were tightly associated with mountain mossy forest and scrubland above 2,000 m, facilitating the prediction of their past and future distributions. The genetic analysis supports a Holocene fragmentation of a larger population into smaller ones that are now isolated in interglacial refugia on mountaintops. These findings are consistent with climatic reconstructions and the retreat of upland forest to higher elevations after the Last Glacial Maximum (LGM), ~21 kya.

Main conclusions

The two isolated populations of summit rats formed through the upland shift of their habitat after the LGM. The current trend of global warming will likely lead to diminishing suitable upland habitat and result in the extinction of the population on Mt. Tambuyukon. The population on Mt. Kinabalu, the higher peak, could persist at higher elevations, highlighting the singular value of high tropical mountains as reservoirs of biodiversity during past and ongoing climate change.

     

Combining ecological niche modelling and morphology to assess the range‐wide population genetic structure of bobcats (Lynx rufus)

Despite a broad distribution, general habitat requirements, and a large dispersal potential, bobcats (Lynx rufus) exhibit a genetic division that longitudinally transects central North America. We investigated (1) whether the climate of the Last Glacial Maximum (LGM; 21 kya) isolated bobcats into refugia and also whether the current climate influences gene flow between the segregate populations and (2) whether the geographical patterns in cranial morphology reflect population identity. We created ecological niche models (ENMs) to evaluate climatic suitability and to estimate distributions of the disparate populations under both historical (LGM) and contemporary conditions. We used two‐dimensional geometric morphometric methods to evaluate variations in the cranium and mandible. These variations were then regressed across geographical variables to assess morphological differences throughout the range of the bobcat. ENMs projected onto LGM climate provided evidence of refugia during the LGM via increased suitability in the north‐west and south‐east portions of this species' range. Contemporarily, our models suggest that the Great Plains may be restricting bobcat migration and gene flow, effectively maintaining disparate populations. Morphological analyses identified a significant linear trend in shape variation across latitudinal and longitudinal gradients rather than distinct morphological divergence between lineages. Similar shape variations, however, did converge in approximate locations of assumed refugia. The findings of the present study provide a robust assessment of the biogeographical considerations for the population genetic structure of bobcats.     

Did tree‐Betula,Pinus and Picea survive the last glaciation along the west coast of Norway? A review of the evidence,in light of Kullman (2002)

Aim We discuss the hypotheses proposed by Kullman [Geo‐Öko 21 (2000) 141; Nordic Journal of Botany 21 (2001) 39; Journal of Biogeography 29 (2002) 1117] on the basis of radiocarbon‐dated megafossils of late‐glacial age from the central Swedish mountains that boreal trees survived the glaciation along the south‐west coast of Norway and subsequently migrated eastward early in the late‐glacial to early deglaciated parts of the central Swedish Scandes mountains. Methods We assess these hypotheses on the basis of glacial geological evidence and four lines of palaeoecological evidence, namely macrofossil records of the tree species, vegetation and climate reconstructions from plant evidence, independent climate reconstructions from other proxies for the late‐glacial environment of south‐west Norway, and the patterns of post‐glacial spread of the tree species. Location South and west Norway, central Swedish Scandes mountains (Jämtland). Results and conclusions South‐west Norway and the adjacent continental shelf were under ice at the last‐glacial maximum (LGM). The late‐glacial vegetation of south‐west Norway was treeless and summer temperatures were below the thermal limits for Betula pubescens Ehrh., Pinus sylvestris L. and Picea abies (L.) Karst. Instead of spreading immediately after the onset of Holocene warming, as might have been expected if local populations were surviving, B. pubescens showed a lag of local arrival of 600 to > 1000 years, Pinus lagged by 1500 to > 2000 years, and Picea only reached southern Norway c. 1500 years ago and has not colonized most of south‐west Norway west of the watershed. Glacial geological evidence shows the presence of an ice sheet in the Scandes at the LGM and in the Younger Dryas, which was cold‐based near or at the area where the late‐glacial‐dated megafossils were recovered by Kullman. We conclude that the samples dated by Kullman (2002) should be evaluated carefully for possible sources of contamination. All the available evidence shows that the biogeographical hypotheses, based on these radiocarbon dates taken at face value, of late‐glacial tree survival at the Norwegian coast and subsequent eastwards spread to the mountains, are unsupportable.     

A new Late-glacial site with Picea abies in the northern Apennine foothills: an exception to the model of glacial refugia of trees

We describe a new palaeobotanical site at Bubano quarry on the easternmost Po plain, northern Italy. Pollen and macrofossils from river and marsh sediments demonstrate the occurrence of Picea in a Pinus sylvestris forest growing in a radius of some tens of kilometres south of the sedimentation place, at the beginning of the Late-glacial interstadial. The Late-glacial and Holocene history of Picea in the northern Apennines is reconstructed on the basis of the palaeobotanical record. The sharp climatic continentality increase eastwards across the northern Apennines from the Tyrrhenian to the Adriatic coast is considered significant for the survival of Picea during the Late-glacial. The most critical phase of survival is related to the moisture changes and consequent Abies competition associated with the last glacial-interglacial transition and the early Holocene. The residual spruce populations expanded during the middle Holocene. The history of Picea in the northern Apennines is a case of ineffective interglacial spread of tree populations from pre-existing stands of LGM (Last Glacial Maximum) and Late-glacial age.     

Breach of the northern Rocky Mountain geoclimatic barrier: initiation of range expansion by the mountain pine beetle

Aim Our aim is to examine the historical breach of the geoclimatic barrier of the Rocky Mountains by the mountain pine beetle (Dendroctonus ponderosae Hopkins). This recent range expansion from west of the North American continental divide into the eastern boreal forest threatens to provide a conduit to naïve pine hosts in eastern North America. We examine the initial expansion events and determine potential mechanism(s) of spread by comparing spread patterns in consecutive years to various dispersal hypotheses such as: (1) meso‐scale atmospheric dispersal of insects from source populations south‐west of the Rocky Mountains in British Columbia (i.e. their historical range), (2) anthropogenic transport of infested plant material, and (3) spread of insect populations across adjacent stands via corridors of suitable habitat. Location British Columbia, Canada. Methods We explore potential mechanism(s) of invasion of the mountain pine beetle using spatial point process models for the initial 3 years of landscape‐level data collection, 2004–2006. Specifically, we examine observed patterns of infestation relative to covariates reflecting various dispersal hypotheses. We select the most parsimonious models for each of the initial 3 years of invasion using information criteria statistics. Results The initial range expansion and invasion of the beetle was characterized by aerial deposition along a strong north‐west to south‐east gradient, with additional aerial deposition and localized dispersal from persisting populations in following years. Main conclusions Following deposition of a wave front of mountain pine beetles parallel to the Rocky Mountains via meso‐scale atmospheric dispersal, the areas of highest intensity of infestations advanced up to 25 km north‐east towards jack pine (Pinus banksiana) habitat in a single year. There appeared to be no association between putative anthropogenic movement of infested materials and initial range expansion of the mountain pine beetle across the continental divide.