Quaternary Climatic Fluctuations Research Articles

Intraspecific differentiation of Allium wallichii (Amaryllidaceae) inferred from chloroplast DNA and internal transcribed spacer fragments

AbstractIn the present study, we used two chloroplast DNA (cpDNA) fragments (trnL‐F and rps16) and the nuclear ribosomal internal transcribed spacer (ITS) sequence data to examine intraspecific differentiation and phylogeographical history of Allium wallichii. Based on wide scale sampling (28 populations and 174 individuals) across the entire distribution range of this species, 33 cpDNA haplotypes and 25 ITS ribotypes were detected in our investigation. These cpDNA haplotypes were divided into three major lineages, which was further supported by the ITS phylogenetic results. High haplotype/ribotype diversity and population differentiation, together with most of the haplotypes/ribotypes being exclusive to single populations, implied restricted gene flow among populations and significant geographical isolation. Nearly all populations with high haplotype/ribotype diversity were found in the Hengduan Mountain Region (HMR), whereas the populations of the Himalayas and Nanling Mountains showed a lower level, suggesting the HMR might serve as a potential divergence center for A. wallichii. The main lineages of A. wallichii diverged from each other between Mid–Late Pliocene and Early Quaternary based on two sets of molecular markers, indicating that the Quaternary climatic fluctuation could not have contributed greatly to the divergence of the main lineages of A. wallichii. Instead, the intricate topography and heterogeneous habitats resulting from the drastic uplift of the Qinghai–Tibet Plateau from the Late Pliocene could be responsible for the intraspecific differentiation of A. wallichii. The present study further highlights the importance of geographic isolation and habitat heterogeneity in shaping and maintaining high species diversity within the HMR.

Tertiary Origin and Pleistocene Diversification of Dragon Blood Tree (Dracaena cambodiana-Asparagaceae) Populations in the Asian Tropical Forests

BackgroundThe origin of extraordinarily rich biodiversity in tropical forests is often attributed to evolution under stable climatic conditions over a long period or to climatic fluctuations during the recent Quaternary period. Here, we test these two hypotheses using Dracaena cambodiana, a plant species distributed in paleotropical forests.MethodsWe analyzed nucleotide sequence data of two chloroplast DNA (cpDNA: atpB-rbcL and trnD-trnT) regions and genotype data of six nuclear microsatellites from 15 populations (140 and 363 individuals, respectively) distributed in Indochina Peninsular and Hainan Island to infer the patterns of genetic diversity and phylogeographic structure. The population bottleneck and genetic drift were estimated based upon nuclear microsatellites data using the software programs BOTTLENECK and 2MOD. The lineage divergence times and past population dynamics based on cpDNA data were estimated using coalescent-based isolation-with-migration (IMa) and BEAST software programs.ResultsA significant phylogeographic structure (N ST = 0.876, G ST = 0.796, F ST-SSR = 0.329, R ST = 0.449; N ST>G ST, R ST>F ST-SSR, P<0.05) and genetic differentiation among populations were detected. Bottleneck analyses and Bayesian skyline plot suggested recent population reduction. The cpDNA haplotype network revealed the ancestral populations from the southern Indochina region expanded to northward. The most recent ancestor divergence time of D. cambodiana dated back to the Tertiary era and rapid diversification of terminal lineages corresponded to the Quaternary period.ConclusionsThe results indicated that the present distribution of genetic diversity in D. cambodiana was an outcome of Tertiary dispersal and rapid divergence during the Quaternary period under limited gene flow influenced by the uplift of Himalayan-Tibetan Plateau and Quaternary climatic fluctuations respectively. Evolutionary processes, such as extinction-recolonization during the Pleistocene may have contributed to the fast diversification in D. cambodiana.

Soil–landscape response to mid and late Quaternary climate fluctuations based on numerical simulations

We use a numerical dynamic soil–landscape model to study one aspect of the spatio-temporal soil–landscape evolution process, the effect of climatic fluctuations on soil grading distribution in space and time in response to the interplay between physical weathering and surface erosion (soil mineralogical fluxes). We simulate a synthetic soil–landscape system over the middle and late Quaternary (last 400ka). The results show that (1) soil–landscape response to climate change is non-linear and highly spatially variable, even at hillslope scale; and (2) soil–landscape adjustment to climate change can lag tens of thousands of years and is both spatially and temporally variable. We propose that the legacy of past climatic condition (i.e. last glacial maximum) in modern soil–landscape systems vary considerably in space. This implies that the spatiotemporal uniformity in which soil is typically described in Earth system modeling and analysis (e.g. carbon cycle) grossly underestimates their actual complexity.

Temporal genetic variation of the red fox, Vulpes vulpes, across western Europe and the British Isles

Quaternary climatic fluctuations have had profound effects on the phylogeographic structure of many species. Classically, species were thought to have become isolated in peninsular refugia, but there is limited evidence that large, non-polar species survived outside traditional refugial areas. We examined the phylogeographic structure of the red fox (Vulpes vulpes), a species that shows high ecological adaptability in the western Palaearctic region. We compared mitochondrial DNA sequences (cytochrome b and control region) from 399 modern and 31 ancient individuals from across Europe. Our objective was to test whether red foxes colonised the British Isles from mainland Europe in the late Pleistocene, or whether there is evidence that they persisted in the region through the Last Glacial Maximum.We found red foxes to show a high degree of phylogeographic structuring across Europe and, consistent with palaeontological and ancient DNA evidence, confirmed via phylogenetic indicators that red foxes were persistent in areas outside peninsular refugia during the last ice age. Bayesian analyses and tests of neutrality indicated population expansion. We conclude that there is evidence that red foxes from the British Isles derived from central European populations that became isolated after the closure of the landbridge with Europe.

Quaternary biostratigraphy and biochronology of the West Siberian plain: trans-regional and trans-zonal correlations

Summarized information is given on the Upper Pliocene–Pleistocene deposits of the Southern Urals with data on the distribution of significant ostracod species, molluscs, large and small mammals and plant remains.The Late Cenozoic history of the Southern Urals is characterized by transgression of the Akchagylian Sea, which ingressed all river valleys of the Southern Fore-Urals during the Pliocene. The Pleistocene deposits in the area are of continental origin. The Pleistocene cover glaciations did not reach the Southern Urals; however, the Quaternary climatic fluctuations affected the history of the fauna, flora and human societies, as well as the geomorphological character of the area. The development of the territory was governed by a general activization of tectonic movements and a quick uplift of the surface. This event belongs to the most recent stage of the geological history of the Urals. According to recent fission-track data, the age of the relics of a peneplain preserved in the tops of the Ural Mountains is hardly older than the Cretaceous, which contradicts the traditional point of view. The period of formation of the modern Ural Mountains is probably also much shorter than is usually thought and corresponds mainly to Pliocene-Quaternary times.The Southern Urals is an important area for correlation between the European and Siberian/Asiatic stratigraphic schemes. To improve the correlation between these two areas and to expand our understanding of the complex geology of the area, future (bio)stratigraphical investigation of the Pliocene–Pleistocene deposits of the Southern Urals region is necessary.

Phylogeography of the Vipera ursinii complex (Viperidae): mitochondrial markers reveal an east–west disjunction in the Palaearctic region

AbstractAim The aim of this study was to elucidate the phylogeographical pattern of taxa composing the Vipera ursinii complex, for which the taxonomic status and the dating of splitting events have been the subject of much debate. The objectives were to delimit potential refugia and to date splitting events in order to suggest a scenario that explains the diversification of this species complex.Location Western Europe to Central Asia.Methods Sequences of the mitochondrial cytochrome b and NADH dehydrogenase subunit 4 (ND4) genes were analysed for 125 individuals from 46 locations throughout the distribution range of the complex. The phylogeographical structure was investigated using Bayesian and maximum likelihood methods. Molecular dating was performed using three calibration points to estimate the timing of diversification.Results Eighty‐nine haplotypes were observed from the concatenation of the two genes. Phylogenetic inferences supported two main groups, referred to in this study as the ‘ursinii clade’ and the ‘renardi clade’, within which several subclades were identified. Samples from Greece (Vipera ursinii graeca) represented the first split within the V. ursinii complex. In addition, three main periods of diversification were revealed, mainly during the Pleistocene (2.4–2.0 Ma, 1.4 Ma and 1.0–0.6 Ma).Main conclusions The present distribution of the V. ursinii complex seems to have been shaped by Quaternary climatic fluctuations, and the Balkan, Caucasus and Carpathian regions are identified in this study as probable refugia. Our results support a south–north pattern of colonization, in contrast to the north–south colonization previously proposed for this complex. The biogeographical history of the V. ursinii complex corroborates other biogeographical studies that have revealed an east–west disjunction (situated near the Black Sea) within a species complex distributed throughout the Palaearctic region.

Climatic stability in the Brazilian Cerrado: implications for biogeographical connections of South American savannas, species richness and conservation in a biodiversity hotspot

AbstractAim To investigate the historical distribution of the Cerrado across Quaternary climatic fluctuations and to generate historical stability maps to test: (1) whether the ‘historical climate’ stability hypothesis explains squamate reptile richness in the Cerrado; and (2) the hypothesis of Pleistocene connections between savannas located north and south of Amazonia.Location The Cerrado, a savanna biome and a global biodiversity hotspot distributed mainly in central Brazil.Methods We generated occurrence datasets from 1000 presence points randomly selected from the entire distribution of the Cerrado, as determined by two spatial definitions. We modelled the potential Cerrado distribution by implementing a maximum‐entropy machine‐learning algorithm across four time projections: current, mid‐Holocene (6 ka), Last Glacial Maximum (LGM, 21 ka) and Last Interglacial (LIG, 120 ka). We generated historical stability maps (refugial areas) by overlapping presence/absence projections of all scenarios, and checked consistencies with qualitative comparisons with available fossil pollen records. We built a spatially explicit simultaneous autoregressive model to explore the relationship between current climate, climatic stability, and squamate species richness.Results Models predicted the LGM and LIG as the periods of narrowest and widest Cerrado distributions, respectively, and were largely corroborated by palynological evidence. We found evidence for two savanna corridors (eastern coastal during the LIG, and Andean during the LGM) and predicted a large refugial area in the north‐eastern Cerrado (Serra Geral de Goiás refugium). Variables related to climatic stability predicted squamate richness better than present climatic variables did.Main conclusions Our results indicate that Bolivian savannas should be included within the Cerrado range and that the Cerrado’s biogeographical counterparts are not Chaco and Caatinga but rather the disjunct savannas of the Guyana shield plateaus. Climatic stability is a good predictor of Cerrado squamate richness, and our stability maps could be used in future studies to test diversity patterns and genetic signatures of different taxonomic groups and as a higher‐order landscape biodiversity surrogate for conservation planning.

Defining spatial and temporal patterns of phylogeographic structure in Madagascar’s iguanid lizards (genus Oplurus)

Understanding the remarkably high species diversity and levels of endemism found among Madagascar's flora and fauna has been the focus of many studies. One hypothesis that has received much attention proposes that Quaternary climate fluctuations spurred diversification. While spatial patterns of distribution and phylogenetic relationships can provide support for biogeographic predictions, temporal estimates of divergence are required to determine the fit of these geospatial patterns to climatic or biogeographic mechanisms. We use multilocus DNA sequence data to test whether divergence times among Malagasy iguanid lizards of the subfamily Oplurinae are compatible with a hypotheses of Pliocene-Pleistocene diversification. We estimate the oplurine species tree and associated divergence times under a relaxed-clock model. In addition, we examine the phylogeographic structure and population divergence times within two sister species of Oplurus primarily distributed in the north-west and south-west of Madagascar (Oplurus cuvieri and Oplurus cyclurus, respectively). We find that divergence events among oplurine lineages occurred in the Oligocene and Miocene and are thus far older and incompatible with the hypothesis that recent climate fluctuations are related to current species diversity. However, the timing of intraspecific divergences and spatial patterns of population genetic structure within O.cuvieri and O.cyclurus suggest a role for both intrinsic barriers and recent climate fluctuations at population-level divergences. Integrating information across spatial and temporal scales allows us to identify and better understand the mechanisms generating patterns diversity.

The River Mondego terraces at the Figueira da Foz coastal area (western central Portugal): Geomorphological and sedimentological characterization of a terrace staircase affected by differential uplift and glacio-eustasy

A geomorphological and sedimentological characterization of the River Mondego terraces in the Figueira da Foz coastal area, Portugal, is presented. The relief is dominated by a Pliocene a marine sandy unit ~10–15m thick, reaching ~250ma.s.l., that covers a shore platform surface. The River Mondego has incised into the Pliocene relief and its long drainage evolution is recorded within a series of inset river terrace landforms. These river terraces are better preserved on the right-hand (northern) bank, where they form a staircase developed against the uplifted Serra da Boa Viagem structure. A set of five river terraces, represented by sedimentary deposits or erosional straths, are identified, namely: T1 at 128–125m; T2 at 101–90m; T3 at 70–60m; T4 at 29–24m; T5 at 11–10ma.s.l. Some luminescence dating ages were obtained from the river terrace deposits: >390ka from the middle of T4; >170ka from the top of T4; ~120ka from the base of T5; ~109ka from T5 (average age for three samples); and 53±3ka from a colluvium at 35ma.s.l. Some differences in altitude of the uppermost sedimentary unit and of the terraces are here interpreted as resulting from vertical displacements of active faults during the Quaternary. The main tectonic structure is the WNW–ESE trending Quiaios fault, responsible for the regional tilting towards SW. Other probably active faults and tectonic lineaments trend NNW–SSE to N–S, NNE–SSW to NE–SW and WNW–ESE. This study reports a long-term uplift rate of 0.004–0.055m/ka for the last 3.6Ma, but 0.017–0.118m/ka for the last ~1.8Ma (using as references, respectively, the base and the surface of the uppermost sedimentary unit). The facies associations that characterize the older terrace deposits (T1 and T2) consist of poorly sorted fluvial sandy-gravels and silts, but also some colluvium at the top of each terrace. The younger terraces (T3, T4 and T5) show better developed sedimentary structures and less sedimentary matrix; the sedimentary features are indicative of both fluvial and coastal environments (estuary and beach, as nowadays). Under conditions of continuous uplift, the episodes of river down-cutting, valley widening and aggradation in the studied area can be attributed to the rise and fall of sea-level in response to the global Quaternary climatic fluctuations. Considering the number of terraces and the dating obtained, it seems that the control of terrace genesis in this coastal area should be dominated by glacio-eustasy whereby episodic valley incision would have been determined by periods of very low sea-level, probably at ~460–410ka (T3/T4; MIS12), ~200–125ka (T4/T5; MIS6) and 100–14ka (T5/Recent alluvial infill; late MIS5, MIS4, MIS3 and MIS2). Some sandy colluvium deposits on the slopes are probably related with mild-cold and wet climate conditions during the period 60 to 32ka. The aeolian dunes are younger (cold to temperate dry conditions; MIS2 and MIS1).

Vegetazione e clima nel Bacino mediterraneo durante l'Olocene

Vegetation and climate in the Mediterranean Basin during the Holocene.The Holocene history of the Mediterranean regions has been influenced by multiple factors, including Quaternary climate fluctuations, complex geographical and physiographical situations, and a long history of human occupations. Interactions among these factors make it often difficult to reconstruct the Holocene climate fluctuations from the vegetational changes recorded by pollen data. The modern vegetation depends not only on climatic factors, determining the distribution of vegetation in latitudinal and longitudinal belts, but also on the location of the refuge areas where temperate forests could withstand the driest phases of the last glacial period and from where they spread during the postglacial. In the Mediterranean regions, the human occupations since the Palaeolithic determined significant changes in the vegetational landscape, through clearance, agriculture, livestock breeding and fires, which often obliterate the responses of plant species to natural factors.During the lateglacial and early Holocene (15-9 cal ka BP) the vegetation changes in relation to climate flutuations were geographically much diversified. In mountain areas, the expansion of dense mixed forest vegetation in areas previously occupied by steppe and grasslands started already around 13.7 cal ka BP (Huntley et alii, 1999; Magri, 1999), while in southern Mediterranean regions (Sicily: Sadori & Narcisi, 2001; Morocco: Rhoujjati et alii, 2010; Lebanon: Hajar et alii, 2010) the reafforestation process occurred after 11 ka BP. In spite of this regional variability, it is possible to recognise vegetational fluctuations recorded in large regions of the Mediterranean Basin. For example, around 4 ka BP a temporary reduction of the evergreen vegetation has been recorded in several pollen records of the Central Mediterranean regions south of 43°N, possibly driven by the northward progression of a north African high pressure cell (Di Rita & Magri, 2009). Since the mid-Holocene, a general increase of the evergreen elements is observed, especially in the most arid areas of the Mediterranean basin (Jahns, 1993; Jalut et alii, 2000; Sadori & Narcisi, 2001; Di Rita & Magri, 2009; Di Rita et alii, 2011).In historical times, the demographic increase and the diffusion of human activities have certainly determined considerable changes in the vegetational landscape, so that it is very difficult to identify any climate change from the pollen records. Even so, it cannot be excluded that some recent vegetational changes may be caused by natural rather than human factors.The discussion on timing, modes and trends in the Holocene vegetation dynamics of the Mediterranean regions is very lively and offers the intriguing possibility of multidisciplinary interpretations of complex phenomena, so contributing to the study on the ongoing climate changes and to management and conservation actions of one of the most important biodiversity hotspots in the world.

Persistence in Peripheral Refugia Promotes Phenotypic Divergence and Speciation in a Rainforest Frog

It is well established from the fossil record and phylogeographic analyses that late Quaternary climate fluctuations led to substantial changes in species' distribution, but whether and how these fluctuations resulted in phenotypic divergence and speciation is less clear. This question can be addressed through detailed analysis of traits relevant to ecology and mating within and among intraspecific lineages that persisted in separate refugia. In a biogeographic system (the Australian Wet Tropics [AWT]) with a well-established history of refugial isolation during Pleistocene glacial periods, we tested whether climate-mediated changes in distribution drove genetic and phenotypic divergence in the rainforest frog Cophixalus ornatus. We combined paleomodeling and multilocus genetics to demonstrate long-term persistence within, and isolation among, one central and two peripheral refugia. In contrast to other AWT vertebrates, the three major lineages differ in ecologically relevant morphology and in mating call, reflecting divergent selection and/or genetic drift in the peripheral isolates. Divergence in mating call and contact zone analyses suggest that the lineages now represent distinct species. The results show that climate shifts can promote genetic and phenotypic divergence and, potentially, speciation and direct attention toward incorporating adaptive traits into phylogeographic studies to better resolve the mechanisms of speciation.

The legacy of ice ages in mountain species: post-glacial colonization of mountain tops rather than current range fragmentation determines mitochondrial genetic diversity in an endemic Pyrenean rock lizard

Aim The genetic impact of Quaternary climatic fluctuations on mountain endemic species has rarely been investigated. The Pyrenean rock lizard (Iberolacerta bonnali) is restricted to alpine habitats in the Pyrenees where it exhibits a highly fragmented distribution between massifs and between habitats within massifs. Using mitochondrial DNA markers, we set out: (1) to test whether several evolutionary units exist within the species; (2) to understand how the species persisted through the Last Glacial Maximum and whether the current range fragmentation originates from distribution shifts after the Last Glacial Maximum or from more ancient events; and (3) to investigate whether current mitochondrial diversity reflects past population history or current habitat fragmentation. Location The Pyrenees in south-western France and northern Spain. Methods We used variation in the hypervariable left domain of the mitochondrial control region of 146 lizards collected in 15 localities, supplemented by cytochrome b sequences downloaded from GenBank to cover most of the species’ distribution range. Measures of population genetic diversity were contrasted with population isolation inferred from topography. Classical (F-statistics) and coalescence-based methods were used to assess the level of gene flow and estimate divergence time between populations. We used coalescence-based simulations to test the congruence of our genetic data with a scenario of simultaneous divergence of current populations. Results Coalescence-based analyses suggested that these peripheral populations diverged simultaneously at the end of the last glacial episode when their habitats became isolated on mountain summits. High mitochondrial diversity was found in peripheral, isolated populations, while the populations from the core of the species’ range were genetically impoverished. Where mitochondrial diversity has been retained, populations within the same massif exhibited high levels of genetic differentiation. Main conclusions As suggested for many other mountain species, the Pyrenean rock lizard survived glacial maxima through short-distance range shifts instead of migration or contraction in distant southern refugia. Most of the main Pyrenean range has apparently been re-colonized from a single or a few source populations, resulting in a loss of genetic diversity in re-colonized areas. As a result, current levels of intra-population mitochondrial diversity are better explained by post-glacial population history than by current habitat fragmentation. Genetic population differentiation within massifs implies severe reduction in female-mediated gene flow between patches of habitats.

Genetic structure of Brachidontes puniceus populations in Cape Verde archipelago shows signature of expansion during the last glacial maximum

Quaternary climatic fluctuations had major impacts on species’ distributions over the last 2.5 Myr. Expansions and contractions of the polar ice caps throughout glacial cycles strongly affected terrestrial fauna and flora whereas eustatic sea level variations had major consequences on rocky-shore communities. The effect of these glacial episodes on marine organisms inhabiting oceanic islands is still poorly understood. We analysed the genetic structure of the marine mussel Brachidontes puniceus from the Cape Verde Islands using mitochondrial sequence data. The apparent absence of physical oceanographic barriers or ecological filters in the geographical range of B. puniceus is reflected in the lack of genetic structure found among populations from the entire archipelago. Larval dispersal in B. puniceus likely played a critical role in the demographic connectivity of populations across the Cape Verde archipelago. Results from demographic analysis were consistent with a population expansion promoted by an increase in the habitat available for larval settlement resulting from a low sea-level stand during the last glacial maximum.

Revisiting the historical distribution of Seasonally Dry Tropical Forests: new insights based on palaeodistribution modelling and palynological evidencegeb

Aim To investigate the potential distribution of Seasonally Dry Tropical Forests (SDTFs) during the Quaternary climatic fluctuations; to reassess the formerly proposed ‘Pleistocenic arc hypothesis’ (PAH); and to identify historically stable and unstable areas of SDTF distributions in the light of palaeodistribution modelling. Location SDTFs in lowland cis-Andean eastern-central South America. Methods We first developed georeferenced maps depicting the current distributional extent of SDTFs under two distinct definitions (narrow and broad). We then generated occurrence datasets, which were used with current and past bioclimatic variables to predict SDTF occurrence by implementing the maximum entropy machine-learning algorithm. We obtained historical stability maps by overlapping the presence/absence projections of each of three climatic scenarios [current, 6 kyr bp during the Holocene, and 21 kyr bp during the Last Glacial Maximum (LGM)]. Finally, we checked the consistencies of the model prediction with qualitative comparisons of vegetation types inferred from available fossil pollen records. Results The present-day SDTF distribution is disjunct, but we provide evidence that it was even more disjunct during the LGM. Reconstructions support a progressive southward and eastward expansion of SDTFs on a continental scale since the LGM. No significant expansion of SDTFs into the Amazon Basin was detected. Areas of presumed long-term stability are identified and confirmed (the three nuclear regions, Caatinga, Misiones and Piedmont, plus the Chiquitano region), and these possibly acted as current and historical refugial areas. Main conclusions The LGM climate was probably too dry and cold to support large tracts of SDTF, which were restricted to climatically favourable areas relative to the present day (in contrast with the PAH, as it was originally conceived). Expansions of SDTFs are proposed to have occupied the southern portion of Caatinga nucleus more recently during the early–middle Holocene transition. We propose an alternative scenario amenable to further testing of an earlier SDTF expansion (either at the Lower Pleistocene or the Tertiary), followed by fragmentation in the LGM and secondary expansion in the Holocene. The stability maps were used to generate specific genetic predictions at both continental and regional scales (stable areas are expected to have higher genetic diversity and endemism levels than adjacent unstable areas) that can be used to direct field sampling to cover both stable (predicted refugia) and unstable (recently colonized) areas. Lastly, we discuss the possibility that SDTFs may experience future expansion under changing climate scenarios and that both stable and unstable areas should be prioritized by conservation initiatives.

Historical biogeography of western heather voles (Phenacomys intermedius) in montane systems of the Pacific Northwest

Quaternary climate fluctuations and topographical variation in the Pacific Northwest region of North America have interacted to affect the historical biogeography of biota in this region. High-elevation mammals have unique diversification patterns due to their isolation on mountaintops and potential for population growth and range expansion in lowland refugia that are available during glacial periods. We examined the phylogeographic structure, dates of lineage diversification, and historical demography of western heather vole (Phenacomys intermedius) populations across several mountain ranges in the Pacific Northwest. Our analysis of sequence variation in the mitochondrial control region using both maximum-likelihood and Bayesian methods identified 3 major geographically distinct lineages: an Oregon and California lineage, Washington lineage, and Northern and Interior lineage. Our estimate of divergence times using a Bayesian relaxed molecular-clock method revealed that diversification among these major lineages began ∼1.8 million years ago (mya) in the early Pleistocene with the split of the Oregon and California lineage followed by the split of the Washington lineage and the Northern and Interior lineage ∼1.5 mya. All 3 clades remain allopatric, suggesting that they did not share a common refugium during cold climatic intervals of the Pleistocene. Further diversification within each major clade occurred in the middle Pleistocene when populations in isolated mountain ranges became distinct. Demographic estimates from Bayesian skyline plots indicate that each of the 3 major clades has experienced population decline since the early Holocene, possibly due to the redistribution of populations into higher-elevation habitats that became restricted to mountaintops following continental and alpine deglaciation.

Climatic niche and neutral genetic diversity of the six Iberian pine species: a retrospective and prospective view

Quaternary climatic fluctuations have left contrasting historical footprints on the neutral genetic diversity patterns of existing populations of different tree species. We should expect the demography, and consequently the neutral genetic structure, of taxa less tolerant to particular climatic extremes to be more sensitive to long-term climate fluctuations. We explore this hypothesis here by sampling all six pine species found in the Iberian Peninsula (2464 individuals, 105 populations), using a common set of chloroplast microsatellite markers, and by looking at the association between neutral genetic diversity and species-specific climatic requirements. We found large variation in neutral genetic diversity and structure among Iberian pines, with cold-enduring mountain species (Pinus uncinata, P. sylvestris and P. nigra) showing substantially greater diversity than thermophilous taxa (P. pinea and P. halepensis). Within species, we observed a significant positive correlation between population genetic diversity and summer precipitation for some of the mountain pines. The observed pattern is consistent with the hypotheses that: (i) more thermophilous species have been subjected to stronger demographic fluctuations in the past, as a consequence of their maladaptation to recurrent glacial cold stages; and (ii) altitudinal migrations have allowed the maintenance of large effective population sizes and genetic variation in cold-tolerant species, especially in more humid regions. In the light of these results and hypotheses, we discuss some potential genetic consequences of impending climate change.

Phylogeography of the weasel (Mustela nivalis) in the western-Palaearctic region: combined effects of glacial events and human movements

The Iberian, Italian or Balkan peninsulas have been considered as refugia for numerous mammalian species in response to Quaternary climatic fluctuations in Europe. In addition to this 'southerly refugial model', northern refugia have also been described notably for generalist and cold-tolerant species. Here, we investigated the phylogeographic pattern of the weasel (Mustela nivalis) to assess the impact of Quaternary glaciations on the genetic structure, number and location of refugia as well as to determine the impact of human movements on the colonization of Mediterranean islands. We sequenced 1690 bp from the mitochondrial control region and cytochrome b for 88 weasels distributed throughout the western-Palaearctic region, including five Mediterranean islands. Phylogenetic analyses of combined genes produced a clear phylogeographic pattern with two main lineages. The first lineage included all of the western-continental samples (from Spain to Finland) and shows low levels of genetic structure. Demographic analysis highlighted several characteristics of an expanding group, dated approximately at 116 kiloyears (kyr; Riss glaciation). The genetic pattern suggested a northeastern-European origin from which colonization of southwestern Europe took place. The second lineage was divided into five subgroups and indicated a common origin of insular and Moroccan samples from eastern Europe. Eastern-continental weasels did not exhibit signs of sudden expansion, suggesting stable population size during the last ice ages. The time of expansion of Sicilian and Corsican populations was dated around 10 kyr ago, which supports the hypothesis of an early human intervention in the colonization of Mediterranean islands.

New approaches to understanding late Quaternary climate fluctuations and refugial dynamics in Australian wet tropical rain forests

AbstractAim We created spatially explicit models of palaeovegetation stability for the rain forests of the Australia Wet Tropics. We accounted for the climatic fluctuations of the late Quaternary, improving upon previous palaeovegetation modelling for the region in terms of data, approach and coverage of predictions.Location Australian Wet Tropics.Methods We generated climate‐based distribution models for broad rain forest vegetation types using contemporary and reconstructed ‘pre‐clearing’ vegetation data. Models were projected onto previously published palaeoclimate scenarios dating to c. 18 kyr bp. Vegetation stability was estimated as the average likelihood that a location was suitable for rain forest through all climate scenarios. Uncertainty associated with model projections onto novel environmental conditions was also tracked.Results Upland rain forest was found to be the most stable of the wet forest vegetation types examined. We provide evidence that the lowland rain forests were largely extirpated from the region during the last glacial maximum, with only small, marginally suitable fragments persisting in two areas. Models generated using contemporary vegetation data underestimated the area of environmental space suitable for rain forest in historical time periods. Model uncertainty resulting from projection onto novel environmental conditions was low, but generally increased with the number of years before present being modelled.Main conclusions Climate fluctuations of the late Quaternary probably resulted in dramatic change in the extent of rain forest in the region. Pockets of high‐stability upland rain forest were identified, but extreme bottlenecks of area were predicted for lowland rain forest. These factors are expected to have had a dramatic impact on the historical dynamics of population connectivity and patterns of extinction and recolonization of dependent fauna. Finally, we found that models trained on contemporary vegetation data can be problematic for reconstructing vegetation patterns under novel environmental conditions. Climatic tolerances and the historical extent of vegetation may be underestimated when artificial vegetation boundaries imposed by land clearing are not taken into account.

Phylogeographical Structure of the Neotropical Forest Tree Hymenaea courbaril (Leguminosae: Caesalpinioideae) and Its Relationship with the Vicariant Hymenaea stigonocarpa from Cerrado

The phylogeography of Hymenaea courbaril var. stilbocarpa from Atlantic Forest and riverine forests of the Cerrado biome in central and southeastern Brazil was investigated. The data were compared with those of its congeneric Hymenaea stigonocarpa, a typical tree from savanna. In the Cerrado, H. courbaril var. stilbocarpa is found in sites contiguous with those of H. stigonocarpa, and they share common life-history attributes. The psbC/trnS3 region of the chloroplast DNA was sequenced in 149 individuals of H. courbaril var. stilbocarpa. High genetic variation was found in this species, with the identification of 18 haplotypes, similarly to what was found in H. stigonocarpa with 23 haplotypes in the same geographic region. Populations of H. courbaril var. stilbocarpa could be structured in 3 phylogeographic groups. Spatial analysis of molecular variation indicated that 46.4% of the genetic variation was due to differences among these groups. Three haplotypes were shared by H. courbaril var. stilbocarpa and H. stigonocarpa, and only 10.5% of the total genetic variation could be attributed to between-species difference. We surmise that during the glacial times, H. courbaril var. stilbocarpa populations must have gone extinct in most parts of the southern of its present-day occurrence area. After climate amelioration, these areas were probably recolonized from northern and eastern. The relatively similar phylogeographic structure of vicariant Hymenaea species suggests that they were subjected to the same impacts during the Quaternary climatic fluctuations. The sharing of haplotypes and the genetic similarity between the 2 Hymenaea species suggest the existence of ancestral polymorphism and/or hybridization.

Geomorphic archives of Late Quaternary climatic fluctuations at both borders of the Western Sahara

Although a great number of excellent studies has already provided the best dated and most comprehensive evidence of late Quaternary environmental fluctuations in the tropical deserts, this volume presents five new local or regional geomorphic investigations in the Western Sahara and at its borders. How can we improve our knowledge of the continental chronology, of the duration and the origin of the Late Quaternary alternating dry and humid phases? This exciting research topic requires develop...