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66 results for “glacial refugia”
Data from: Sea-level driven glacial-age refugia and post-glacial mixing on subtropical coasts, a palaeohabitat and genetic study
Using a novel combination of palaeohabitat modelling and genetic mixture analyses, we identify and assess a sea-level-driven recolonization process following the Last Glacial Maximum (LGM). Our palaeohabitat modelling reveals dramatic changes in estuarine habitat distribution along the coast of California (USA) and Baja California (Mexico). At the LGM (approx. 20 kya), when sea level was approximately 130 m lower, the palaeo-shoreline was too steep for tidal estuarine habitat formation, eliminating this habitat type from regions where it is currently most abundant, and limiting such estuaries to a northern and a southern refugium separated by 1000 km. We assess the recolonization of estuaries formed during post-LGM sea-level rise through examination of refugium-associated alleles and approximate Bayesian computation in three species of estuarine fishes. Results reveal sourcing of modern populations from both refugia, which admix in the newly formed habitat between the refuges. We infer a dramatic peak in habitat area between 15 and 10 kya with subsequent decline. Overall, this approach revealed a previously undocumented dynamic and integrated relationship between sea-level change, coastal processes and population genetics. These results extend glacial refugial dynamics to unglaciated subtropical coasts and have significant implications for biotic response to predicted sea-level rise.
Data from: Glacial refugia, recolonisation patterns, and diversification forces in Alpine-endemic Megabunus harvestmen
The Pleistocene climatic fluctuations had a huge impact on all life-forms, and various hypotheses regarding the survival of organisms during glacial periods have been postulated. In the European Alps, evidence has been found in support of refugia outside the ice shield (massifs de refuge) acting as sources for postglacial recolonisation of inner-Alpine areas. In contrast, evidence for survival on nunataks, ice-free areas above the glacier, remains scarce. Here, we combine multivariate genetic analyses with ecological niche models (ENMs) through multiple timescales to elucidate the history of alpine Megabunus harvestmen throughout the ice ages, a genus that comprises eight high altitude endemics. ENMs suggest two types of refugia throughout the Last Glacial Maximum, inner-Alpine survival on nunataks for four species and peripheral refugia for further four species. In some geographic regions, the patterns of genetic variation are consistent with long-distance dispersal out of massifs de refuge, repeatedly coupled with geographic parthenogenesis. In other regions, long-term persistence in nunataks may dominate the patterns of genetic divergence. Overall, our results suggest that glacial cycles contributed to allopatric diversification in Alpine Megabunus, both within and at the margins of the ice shield. These findings exemplify the power of ENM projections coupled with genetic analyses to identify hypotheses about the position and number of glacial refugia and thus to evaluate the role of Pleistocene glaciations in driving species-specific responses of recolonisation or persistence that may have contributed to observed patterns of biodiversity.
Data from: Approximate Bayesian computation analysis of EST-associated microsatellites indicates that the broadleaved evergreen tree Castanopsis sieboldii survived the Last Glacial Maximum in multiple refugia in Japan
Climatic changes have played major roles in plants' evolutionary history. Glacial oscillations have been particularly important, but some of their effects on plants' populations are poorly understood, including the numbers and locations of refugia in Asian warm temperate zones. In the present study, we investigated the demographic history of the broadleaved evergreen tree species Castanopsis sieboldii (Fagaceae) during the last glacial period in Japan. We used approximate Bayesian computation (ABC) for model comparison and parameter estimation for the demographic modelling using 27 EST associated microsatellites. We also performed the species distribution modelling (SDM). The results strongly support a demographic scenario that the Ryukyu Islands and the western parts in the main islands (Kyushu and western Shikoku) were derived from separate refugia and the eastern parts in the main islands and the Japan Sea groups were diverged from the western parts prior to the coldest stage of the Last Glacial Maximum (LGM). Our data indicate that multiple refugia survived at least one in the Ryukyu Islands, and the other three regions of the western and eastern parts and around the Japan Sea of the main islands of Japan during the LGM. The SDM analysis also suggests the potential habitats under LGM climate conditions were mainly located along the Pacific Ocean side of coastal region. Our ABC-based study helps efforts resolve the demographic history of a dominant species in warm temperate broadleaved forests during and after the last glacial period, which provides a basic model for future phylogeographical studies using this approach.
Data from: Unravelling the evolutionary history and future prospects of endemic species restricted to former glacial refugia
The contemporary distribution and genetic composition of biodiversity bear a signature of species' evolutionary histories and the effects of past climatic oscillations. For many European species, the Mediterranean peninsulas of Iberia, Italy and the Balkans acted as glacial refugia and the source of range recolonization, and as a result, they contain disproportionately high levels of diversity. As these areas are particularly threatened by future climate change, it is important to understand how past climatic changes affected their biodiversity. We use an integrated approach, combining markers with different evolutionary rates and combining phylogenetic analysis with approximate Bayesian computation and species distribution modelling across temporal scales. We relate phylogeographic processes to patterns of genetic variation in Myotis escalerai, a bat species endemic to the Iberian Peninsula. We found a distinct population structure at the mitochondrial level with a strong geographic signature, indicating lineage divergence into separate glacial refugia within the Iberian refugium. However, microsatellite markers suggest higher levels of gene flow resulting in more limited structure at recent time frames. The evolutionary history of M. escalerai was shaped by the effects of climatic oscillations and changes in forest cover and composition, while its future is threatened by climatically induced range contractions and the role of ecological barriers due to competition interactions in restricting its distribution. This study warns that Mediterranean peninsulas, which provided refuge for European biodiversity during past glaciation events, may become a trap for limited dispersal and ecologically limited endemic species under future climate change, resulting in loss of entire lineages.
Data from: Post-glacial recolonization of the North American Arctic by Arctic char (Salvelinus alpinus): genetic evidence of multiple northern refugia and hybridization between glacial lineages
Aims: We investigated post-glacial recolonization of the North American Arctic by Arctic char (Salvelinus alpinus) and examined potential hybridization between different glacial lineages upon secondary contact. Location: North American Arctic and adjacent areas. Methods: We collected mtDNA sequence data from 1355 individuals from 110 sampling locations and data from nine microsatellite loci from 931 individuals from 37 locations. We assessed the phylogenetic relationships and geographical distribution of mtDNA haplotypes and conducted historical demographic analyses. We used a Bayesian clustering analysis method to detect potential hybridization between glacial lineages. Results: Two highly divergent mtDNA lineages were identified in the Arctic region with distinct but overlapping geographic distributions: one in Beringia and the other over the entire Arctic Archipelago and coastal mainland east of Alaska. The microsatellite data also implied the existence of these two lineages. Evidence of hybridization was detected between the Arctic lineage and an Atlantic lineage in eastern North America. Main conclusions: Our data suggested survival and recolonization from two northern glacial refugia: one in Beringia and another in a smaller refugium, perhaps in the Arctic Archipelago itself or a separate refugium within Beringia. Patterns of hybridization detected supported the presence of a secondary contact zone between glacial lineages in the eastern Canadian Arctic.
From glacial refugia to hydrological microrefugia: factors and processes driving the persistence of the climate relict tree Zelkova sicula
<p>With only two tiny populations, the climate relict <i>Zelkova sicula</i> (Sicily, Italy) is one of the rarest trees in the world. It also represents the most marginal member of genus <i>Zelkova</i> that was widespread in the broadleaved forests thriving in warm-temperate climates throughout Eurasia until the Last Glacial Age. Occurring at the westernmost range of the genus under typical Mediterranean climate, the micro-topographic settings have always appeared crucial for the survival of this Sicilian relict. However, the factors and processes actually involved in its persistence in the current refugia, as well as the response of similar relict trees in arid environments are poorly understood worldwide. In the aim to elucidate these aspects, in the two sites hosting <i>Z. sicula</i> analyses of topographical attributes were combined with investigations on soil moisture dynamics. Additionally, plants' growth and spatial distribution patterns were analysed to detect fine-scale differences between populations and assess the possible ecological amplitude of the species.</p> <p>Results revealed that convergent topographies are basic determinants of microrefugia in arid environments. Within the investigated sites, underground moisture never decreases below 25%, buffering seasonal rainfall fluctuations. Therefore, hydrological microrefugia play a key-role in decoupling from regional climate, supporting the target species in coping with an unsuitable climatic envelope. Additionally, the inter-population variability of biometric attributes showed that individual growth is site-dependent and the species retains a relative ecological plasticity, whereas the strongly clumped spatial patterns confirmed the exclusive vegetative propagation and the common clonal growth. On one hand, deeply incised landforms have acted as effective hydrologic microrefugia, on the other clonality coupled with triploidy supposedly improved the resistance of <i>Z. sicula</i> to harsh environments, though entailing inability to reproduce sexually. Most likely, sterility and environmental/physical barriers prevent since millennia this relict from leaving the last suitable microrefugia, resulting in the two current rear-edge populations.</p>
Supplementary material 2 from: Decker P (2016) Phylogenetic analysis of the Australian trans-Bass Strait millipede genus Pogonosternum (Carl, 1912) (Diplopoda, Polydesmida, Paradoxosomatidae) indicates multiple glacial refugia in southeastern Australia. ZooKeys 578: 15-31. https://doi.org/10.3897/zookeys.578.8052
Alignment of combined dataset : Explanation note: Alignment of the combined COI mtDNA and 16S rRNA dataset
Supplementary material 3 from: Decker P (2016) Phylogenetic analysis of the Australian trans-Bass Strait millipede genus Pogonosternum (Carl, 1912) (Diplopoda, Polydesmida, Paradoxosomatidae) indicates multiple glacial refugia in southeastern Australia. ZooKeys 578: 15-31. https://doi.org/10.3897/zookeys.578.8052
P-distances of combined COI and 16S dataset : Explanation note: Mean uncorrected pairwise distances between terminals (transformed into percentages) of the combined COI mtDNA and 16S rRNA dataset.
Supplementary material 1 from: Decker P (2016) Phylogenetic analysis of the Australian trans-Bass Strait millipede genus Pogonosternum (Carl, 1912) (Diplopoda, Polydesmida, Paradoxosomatidae) indicates multiple glacial refugia in southeastern Australia. ZooKeys 578: 15-31. https://doi.org/10.3897/zookeys.578.8052
Full data of sequenced specimens : Explanation note: Full details of sequenced specimens, including locality, date, collector, collection number and coordinates.
Fig. 6 in From glacial refugia to wide distribution range: demographic expansion of Loropetalum chinense (Hamamelidaceae) in Chinese subtropical evergreen broadleaved forest
Fig. 6 Mismatch distribution analysis detected unimodel distributions with SSD and HRag statistics at the species level
Fig. 4 a in From glacial refugia to wide distribution range: demographic expansion of Loropetalum chinense (Hamamelidaceae) in Chinese subtropical evergreen broadleaved forest
Fig. 4 a Genetic admixture analysis conducted on AFLP data for L. chinense, L. chinense var. rubrum (CUL), and L. subcordatum (LS). Each vertical bar represents an individual and its assignment proportion into one of six population clusters. b Genetic structuring of populations based on AFLP data. The map of the individual assignment in each population to K = 6 clusters (C1–C6) is based on STRUCTURE analysis of the AFLP data. Each cluster is represented by a different color
Data from: Multiple glacial refugia for cool-temperate deciduous trees in northern East Asia: the Mongolian oak as a case study
In East Asia, temperate forests are predicted to have retracted southward to c. 30° N during the last glacial maximum (LGM) based on fossil pollen data, whereas phylogeographic studies have often suggested glacial in situ survival of cool-temperate deciduous trees in their modern northern ranges. Here we report a study of the genetic diversity and structure of 29 natural Mongolian oak (Quercus mongolica) populations using 19 nuclear simple sequence repeat (nSSR) loci and four chloroplast DNA fragments. Bayesian clustering analysis with nSSRs revealed five groups, which were inferred by approximate Bayesian computation (ABC) to have diverged in multiple refugia through multiple glacial–interglacial cycles. Analysis of chloroplast DNA variation revealed four lineages that were largely but incompletely geographically disjunct. Ecological niche modelling (ENMs) indicated a southward range shift of the oak's distribution at the LGM, although high suitability scores were also evident in the Changbai Mts. (Northeast China), the Korean Peninsula, areas surrounding the Bohai Sea, and along the coast of the Russian Far East. In addition, endemic chloroplast DNA haplotypes and nuclear lineages occurred in high-latitude northern areas where the ENM predicted no suitable habitat. The combined evidence from nuclear and chloroplast DNA, and the results of the ENM clearly demonstrate that multiple northern refugia, including cryptic ones, were maintained across the current distributional range of the Mongolian oak during the LGM or earlier glacial periods. Though spatially limited, postglacial expansions from these refugia have led to a pattern of decreased genetic diversity with increasing latitude.
Data from: Lizards on ice: evidence for multiple refugia in Liolaemus pictus (Liolaemidae) during the Last Glacial Maximum in the southern Andean beech forests
Historical climate changes and orogenesis are two important factors that have shaped intraspecific biodiversity patterns worldwide. Although southern South America has experienced such complex events, there is a paucity of studies examining the effects on intraspecific diversification in this part of the world. Liolaemus pictus is the southernmost distributed lizard in the Chilean temperate forest, whose genetic structure has likely been influenced by Pleistocene glaciations. We conducted a phylogeographic study of L. pictus in Chile and Argentina based on one mitochondrial and two nuclear genes, and recovered two strongly divergent groups, Northern and Southern clades, the former distributed from the northernmost limit of the species to the Araucanía region, and the latter being distributed throughout the Andes and the Chiloé archipelago in Southern Chile. Our results suggest that L. pictus originated 751 Kya, with divergence between the two clades occurring in the late Pleistocene. Demographic reconstructions for the Northern and Southern clades indicate a decrease in effective population sizes likely associated with Pleistocene glaciations. Surprisingly, patterns of genetic variation, clades ages and historical gene flow in populations distributed within the limits of the Last Glacial Maximum (LGM) are not explained by recent colonization. We propose an "intra-Andean multiple refuge" hypothesis, along with the classical refuge hypothesis previously proposed for the biota of the Chilean Coastal range and Eastern Andean Cordillera. Our hypothesis is supported by niche modeling analysis suggesting the persistence of fragments of suitable habitat for the species within the limits of the LGM ice shield. This type of refuge hypothesis is proposed for the first time for an ectothermic species.
Data from: Genetic population structure of the round whitefish (Prosopium cylindraceum) in North America: multiple markers reveal glacial refugia and regional subdivision.
Round whitefish (Prosopium cylindraceum) have a broad, disjunct range across northern North America and Eurasia, and little is known about their genetic population structure. We performed genetic analyses of round whitefish from 17 sites across its range using nine microsatellites, two mitochondrial DNA (mtDNA) loci, and 4918 to 8835 single-nucleotide polymorphism (SNP) loci. Our analyses identified deep phylogenetic division between eastern and western portions of the range, likely indicative of origins from at least two separate Pleistocene glacial refugia. Regionally, microsatellites and SNPs identified congruent patterns in subdivision, and population structure was consistent with expectations based on hydrologic connectivity. Within the Laurentian Great Lakes, Lake Huron and Lake Ontario were identified as key areas of interest. Lake Huron appears to be a contemporary source population for several other Great Lakes, and Lake Ontario contains a genetically discrete group of round whitefish. In all cases, multiple genetic markers yielded similar patterns, but SNPs offered substantially enhanced resolution. We conclude that round whitefish have population subdivision on several scales important for understanding their evolutionary history and conservation planning.
The evolution of the Aristolochia pallida complex (Aristolochiaceae) contradicts traditional taxonomy and reflects large-scale glacial refugia in the Mediterranean
<p><span>The taxonomy of the Mediterranean <em>Aristolochia</em> <em>pallida</em> complex has been under debate for several decades with the following species currently recognized: <em>A. pallida, A. lutea, A. nardiana, A. microstoma, A. merxmuelleri, A. croatica </em>and<em> A. castellana</em>. These taxa are distributed from Iberia to Turkey. To reconstruct phylogenetic and biogeographic patterns, we employed cpDNA sequence variation using both non-coding (intron and spacer) and protein-coding regions (i.e. <em>trnK</em> intron, <em>matK</em> gene and <em>trnK</em>-<em>psbA</em> spacer). Our results show that the morphology-based traditional taxonomy was not corroborated by our phylogenetic analyses. <em>Aristolochia pallida, A. lutea, A. nardiana </em>and<em> A. microstoma</em> were not monophyletic. Instead, strong geographic signals were detected. Two major clades, one exclusively occurring in Greece and a second one of pan-Mediterranean distribution, were found. Several subclades distributed in Greece, NW Turkey, Italy, as well as amphi-Adriatic subclades and a subgroup of southern France and Spain were revealed. The distribution areas of these groups are in close vicinity to hypothesised glacial refugia areas in the Mediterranean. According to molecular clock analyses, the diversification of this complex started around 3–3.3 my, before the onset of glaciation cycles, and the further evolution of and within major lineages falls into the Pleistocene. Based on these data, we conclude that the <em>Aristolochia</em> <em>pallida</em> alliance survived in different Mediterranean refugia rarely with low, but often with a high potential for range extension, and a high degree of morphological plasticity.</span></p>
Data from: Genetic population structure of the round whitefish (Prosopium cylindraceum) in North America: multiple markers reveal glacial refugia and regional subdivision.
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Data from: Extending glacial refugia for a European tree: genetic markers show that Iberian populations of white elm are native relicts and not introductions
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Data from: Post-glacial recolonization of the North American Arctic by Arctic char (Salvelinus alpinus): genetic evidence of multiple northern refugia and hybridization between glacial lineages
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Data from: Multiple glacial refugia for cool-temperate deciduous trees in northern East Asia: the Mongolian oak as a case study
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Data from: Sea-level driven glacial-age refugia and post-glacial mixing on subtropical coasts, a palaeohabitat and genetic study
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