Location Of Refugia Research Articles

Glacial history of Saxifragawahlenbergii (Saxifragaceae) in the context of refugial areas in the Western Carpathians.

Despite the wealth of data available for mountain phylogeography, local-scale studies focused on narrow endemic species remain rare. Yet, knowledge of the genetic structure of such species biogeographically linked to a restricted area is of particular importance to understand the history of the local flora and its diversity patterns. Here, we aim to contribute to the phylogeographical overview of the Western Carpathians with a genetic study of Saxifragawahlenbergii, one of the most characteristic endemic species of this region. We sampled populations from all discrete parts of the species' distribution range to apply sequencing of selected non-coding cpDNA and nuclear ribosomal DNA (ITS) regions, as well as Amplified Fragment Length Polymorphism (AFLP) fingerprinting. First, while ITS sequences showed weak diversification, the genetic structure based on cpDNA sequences revealed two well-differentiated groups of haplotypes. One of them is restricted to the main center of the distribution range in the Tatra Mountains (Mts), while the second group included a series of closely related haplotypes, which in most cases were unique for particular isolated groups of populations in peripheral mountain ranges and in the south-eastern part of the Tatra Mts. AFLP fingerprinting also revealed a pattern of divergence among populations, while only partly corroborating the division observed in cpDNA. Taking into account all the data, the pattern of genetic structure, supported by the high levels of unique genetic markers in populations, may reflect the historical isolation of populations in several local refugia during the last glacial period. Not only the center of the range in the Tatra Mts, but also other, neighboring massifs (Malá Fatra, Nízke Tatry, Chočské vrchy, Muránska planina), where populations are characterized by separate plastid DNA haplotypes, could have acted as separate refugia.

Do genetically informed distribution models improve range predictions in past climates? A case study with balsam poplar

Species distribution models (SDMs) are one of the most widely used approaches to predict changes in habitat suitability in response to climate change. However, as typically implemented, SDMs treat species as genetically uniform throughout their ranges and thereby ignore potentially important genetic differences between populations. While numerous studies have used SDMs to model genetically based subgroupings within species, the ability of such models to be transferred to new times has rarely been evaluated. Here, we used standard and genetically informed distribution models (gSDMs) to predict the future and past range of balsam poplar (Populus balsamifera L.). We then assessed model transferability of standard SDMs and gSDMs using balsam poplar fossil pollen and macrofossil occurrences. In general, standard and gSDMs performed similarly through time, with both predicting a northward expanding range from refugia as glaciers receded over the past 22 ky BP and declining suitable area in future climates. Both standard and gSDMs showed moderate abilities to distinguish balsam poplar fossils from pseudo-absences but tended to predict lower suitability at fossil sites during the Pleistocene-Holocene transition. Although gSDMs applied to balsam poplar did not prove more transferable than standard SDMs, they provided numerous unique insights, such as the change in suitable area of genetic clusters through time and potential refugial locations. We argue more research is needed to determine which species may benefit most from the gSDM approach and to test gSDMs with temporally or spatially independent occurrences, as is often recommended for standard SDMs.

Palaeoecological evidence of pollen morphological changes: A climate change adaptation strategy?

Pollen records have been used to reconstruct changes in climate, based on the presence of taxa as proxies for environmental conditions. Pollen grains have morphological features that allow for the identification of different species, genera, and families of flowering plants. However, ecologically distinct species share similar pollen types that may make biogeographic and climate reconstructions problematic. Also, the responses of populations and species to climate changes adjusted through either plasticity or adaptation have been overlooked. Such adjustments are most probably the product of long-lasting in situ persistence in local refugia under favourable microclimates despite hostile regional climate. In southern South America three species of the dominant tree cover of the subgenus Nothofagus are present, two deciduous (N. antarctica and N. pumilio) and one evergreen (N. betuloides), identified in the pollen group Nothofagus dombeyi type. Here we present a pollen record from Punta Arenas (~53°S) that documents significant changes in pollen size that took place during the Late glacial and Early Holocene. The occurrence of smaller Nothofagus dombeyi type pollen grains during the Late glacial may indicate rapid local adaptation to colder and possibly wetter conditions. Our findings are supported by Ecological niche modelling which suggests limited availability of Nothofagus refugia during the Last Glacial Maximum. The local refugia may also have fostered interbreeding between congeneric species that led to unique morphological features that increased the fitness of the recipient pool. We postulate that such modifications were due to the potential transient hybridization between species that later diverged by backcrossing with each deciduous and evergreen taxa.

Mitochondrial Lineage Diversity and Phylogeography of Daphnia (Daphnia) (Crustacea: Cladocera) in North-East Russia

The variability of the 12S gene fragment of the mtDNA for taxa belonging to subgenus Daphnia (Daphnia) O.F. Müller, 1776 (Crustacea: Cladocera) in NE Russia is studied, and their phylogenetic analysis performed. We identified (based both on morphological and molecular data) nine species belonging to four species complexes, namely: (A) D. longispina s.l.: (1) D. longispina O.F. Müller, 1776; (2) D. dentifera Forbes, 1893; (3) D. galeata Sars, 1864; (4) D. umbra Taylor, Hebert et Colbourne, 1996; (B) D. cristata s.l.: (5) D. cristata Sars, 1862; (6) D. longiremis Sars, 1862; (C) D. curvirostris s.l.: (7) D. curvirostris Eylmann, 1887; (D) D. pulex s.l.: (8) D. pulex Leydig, 1860; (9) D. middendorffiana Fischer, 1851. Rare arcto-mountainous taxon D. umbra was found in the mountains of the Sakha (Yakutia) Republic for the first time. Species diversity in NE Asia is relatively low, and the most revealed taxa are trans-Beringian. We also performed a phylogeographic analysis of D. dentifera and D. pulex s.l., the two most common species in NE Russia. Our new data allow us to assume that the daphniids of NE Asia have undergone various evolutionary scenarios during the Pleistocene period: survival is within some local refugia, and re-colonization from these areas and from North America through the Beringian land bridge, etc. We agree with previous authors who revealed that the patterns in the studied species groups are relatively recent (of Late Pleistocene or even Holocene age), although the main phylogenetic daphniid lineages (mainly congruent with the biological species) are very old. Our results provide convincing evidence for the hypothesis that NE Russia is a very important source of modern haplotypic diversity for the cladocerans.

Topographic Complexity Facilitates Persistence Compared to Signals of Contraction and Expansion in the Adjacent Subdued Landscape

Topographically heterogeneous areas are likely to act as refugia for species because they facilitate survival during regional climatic stress due to availability of a range of microenvironments. The Stirling Ranges are a topographically complex area in the generally subdued and ancient landscape of south-western Australia. We investigated the influence of these landscape features on the evolutionary history of the rare woody shrub, Banksia brownii through a combined approach using phylogeographic analysis of sequence data from three chloroplast sequences, the trnV–ndhC, trnQ–rps16, and rpl32–ndhF intergenic spacer regions, and species distribution modeling. The Stirling Ranges showed high genetic diversity and differentiation among populations consistent with localized persistence and maintenance of large populations in an area that species distribution modeling identified as providing habitat stability at the Last Glacial Maximum as well as under warmer conditions. In contrast, populations in the adjacent subdued lowlands showed signals of low diversity, suggesting contraction, and subsequent expansion from localized refugia in the west. Cool summers are an important climatic variable for the species and species distribution modeling showed suitable habitat identified at the LGM suggesting expansion at this time following likely contraction during earlier warmer climatic oscillations. The isolated, coastal population at Vancouver Peninsula showed low diversity but no differentiation and it may have been established in more recent historical times, possibly through Aboriginal movement of seed. Our analysis of B. brownii highlights the complex evolutionary history of the species and the influence of topographic complexity and habitat heterogeneity in this global biodiversity hotspot.

Are fire refugia less predictable due to climate change?

Fire refugia—unburnt habitat within a wildfire’s perimeter—play a key role in wildlife persistence and recovery. While studies have shown that the location of refugia is influenced by local topographic factors, growing evidence points to extreme fire weather becoming the dominant factor driving high-severity wildfires that result in the location of fire refugia being less predictable. Between September 2019 and February 2020, a series of mega-fires in eastern Australia burned largely in broadleaf forest. We assessed burned and unburned areas of forest in eastern Australia using Sentinel-2 satellite data, aggregated monthly over the fire season to calculate a fire severity layer at a 20 m pixel resolution. We found that fires burned 5.7 × 106 ha−1 of forest and woodland. The total percentage area of unburned forest within the wildfire footprint was approximately 10%. The majority (94%) of the unburnt forest and woodland patches within the fire perimeter occurred as patches <1 ha (n = 842 622 and 111 707 ha) with far fewer large unburnt patches (>100 ha) (n = 575 and 286 080 ha). Boosted regression tree analyses of the relationships between fire severity and potential explanatory variables revealed that 63%–78% of the variable importance in the models were climatic and weather-related factors. Fire weather index was the single most important variable for analyses, accounting for 40%–52% of modelled results. Our results reinforce mounting evidence that a shift is underway in the balance between deterministic and contingent factors in the occurrence of fire refugia with local topographic controls being increasingly overridden by severe fire weather conditions, and declining topographic effects as fire severity increases. Further studies are needed over a longer time frame, inclusive of prior forest management impacts, to confirm that the ability to predict fire refugia is permanently declining.

Fine-Scale Spatial Patterns of the Genetic Diversity ofEuropean Beech (Fagus sylvatica L.) around a Mountainous Glacial Refugium in the SW Balkans

Beech (Fagus sylvatica L.) is one of the most important forest trees in Europe and its current broad expanse over the continent is believed to be the outcome of the Holocene postglacial expansion of lineages originating from different glacial refugia. Studies using gene markers, pollen profiles and fossils suggest the main locations of glacial refugia in Southern Europe. In this study, we conduct a fine-scale genetic study on the beech populations surrounding the Almopia basin, an area that is said to have hosted one of the main European glacial refugia for several plant and animal species during the Pleistocene Epoch. We test the hypothesis of the existence of a local refugium in the study area for beech to understand the spatial genetic pattern of the putative refugial beech populations in the area and to investigate possible genetic connections between the local beech populations and the European expansion of the species. The genetic diversity of 100 sampled trees in 20 plots representing the expansion of beech in the area was studied using chloroplast and nuclear DNA microsatellites (cpSSR and nSSR, respectively). All three cpSSR regions were polymorphic, resulting in eight haplotypes, separated spatially in two distinct groups (one on the western and the other on the eastern part of the Almopia basin) that correspond to two different postglacial beech lineages. Furthermore, the cpSSR sequences of the eastern lineage are genetically identical to those of beech populations extending over central and northern Europe. The nSSR markers were highly polymorphic, and the trees studied were separated into two genetic groups that coincided with the cpSSR ones in locations where the topography is more pronounced. These results indicated that the Almopia region was indeed a major refugium for beech that possibly produced two main postglacial lineages for Europe, one of which is connected with the majority of beech populations growing on the continent. These southern refugial populations are important diversity centers that need to be the subject of special management and conservation.

Asymmetric contributions of seed and pollen to gene dispersal in the marsh orchid Dactylorhiza umbrosa in Asia Minor.

Orchids differ from other plants in their extremely small and partly air-filled seeds that can be transported long distances by wind. Seed dispersal in orchids is expected to contribute strongly to overall gene flow, and orchids generally express low levels of genetic differentiation between populations and low pollen to seed flow ratios. However, studies in orchids distributed in northern Europe have often found a poor geographic structuring of genetic variation. Here, we studied geographic differentiation in the marsh orchid Dactylorhiza umbrosa, which is widely distributed in upland regions from Asia Minor to Central Asia. These areas were less affected by Pleistocene ice ages than northern Europe and the orchid should have been able to survive the last ice age in local refugia. In the plastid genome, which is dispersed by seeds, populations at close distance were clearly divergent, but the differentiation still increased with geographic distance, and a significant phylogeographic structure had developed. In the nuclear genome, which is dispersed by both seeds and pollen, populations showed an even stronger correlation between genetic and geographic distance, but average levels of differentiation were lower than in the plastid genome, and no phylogeographic structure was evident. Combining plastid and nuclear data, we found that the ratio of pollen to seed dispersal (mp/ms) decreases with physical distance. Comparison with orchids that grow in parts of Europe that were glaciated during the last ice suggests that a balanced structure of genetic diversity develops only slowly in many terrestrial orchids, despite efficient seed dispersal.

Refugia during the last glacial period and the origin of the disjunct distribution of an insular plant

AbstractAimAlthough many phylogeographic studies have focused on continental refugia, the roles of islands as refugia have long been overlooked. In this study, we conducted phylogeographic studies of a plant with insular distribution, Microtropis japonica, to elucidate the potential roles of islands as refugia during recent glacial periods. Specifically, we test the hypothesis that two remote groups of Japanese islands (the Izu and Ryukyu Islands) were refugia for M japonica.LocationThe Izu and Ryukyu Islands of Japan and their adjacent areas including the Japanese mainland and Taiwan.TaxonMicrotropis japonica (Celastraceae).MethodsA total of 363 individuals were sampled from 44 populations of M japonica. To elucidate population genetic differentiation and demographic change in M japonica, we performed molecular variance and mismatch distribution analyses based on chloroplast DNA (cpDNA) sequence variations and Bayesian clustering and gene flow estimates based on nuclear single‐nucleotide polymorphism (SNP) data. In addition, to examine distribution changes, ecological niche modelling using the maximum entropy method was used to determine suitable habitats existing currently or during the last glacial maximum, using occurrence data and six bioclimatic variables.ResultsBoth cpDNA and nuclear SNP data showed genetic differentiation between two disjunct regions. However, cpDNA data indicated genetic differentiation within the Ryukyu Islands but not within the Izu Islands, while nuclear SNP data indicated genetic differentiation within both island groups. Ecological niche modelling showed that both the Izu and Ryukyu archipelagos had contained some islands with a climate compatible with modern M japonica climate envelopes despite climate oscillations.Main conclusionsIslands within both the Izu and Ryukyu archipelagos may have supported M japonica populations throughout historical climate oscillations. The current disjunct distribution of M japonica strongly reflects its refugial locations during the last glacial period and the subsequent range expansion. Islands were important refuges, contributing to the modern disjunct distribution of M japonica.

Persisting in a glaciated landscape: Pleistocene microrefugia evidenced by the tree wētā Hemideina maori in central South Island, New Zealand

AbstractAimRepeated cycles of Pleistocene glaciation have influenced phylogeographic structure of taxa on New Zealand's South Island. Many taxa became restricted to refugia at either end of the island during glaciation, resulting in an area of low endemicity in central South Island. This area of low endemism is typified by the so‐called beech (or biotic) gap, where the absence of Nothofagus forest (and many other plant and invertebrate taxa) has been attributed to repeated glaciation. Some taxa, however, appear to have persisted in situ in localized refugia within the biotic gap. We test these alternative hypotheses in a large flightless alpine wētā (grasshopper).LocationSouthern Alps, South Island, New Zealand.TaxonHemideina maori Pictet &amp; Saussure, 1891 (Orthoptera: Anostostomatidae).MethodsWe used phylogeographic analysis of mitochondrial cytochrome c oxidase I (cox1) and 25 nuclear DNA (nuDNA) markers to test for Pleistocene glacial microrefugia within the current montane South Island range of Hemideina maori.ResultsWe identified eight deeply differentiated mtDNA lineages with limited sharing of haplotypes among populations. Genetic differentiation assessed using nuDNA revealed a similar pattern, with three groups broadly corresponding to the deepest mtDNA splits. The central South Island region exhibits substantial endemic mtDNA diversity and a distinctive nuclear lineage.Main conclusionsThese results indicate that H. maori likely persisted in microrefugia within the biotic gap during glaciation. These deep lineages are estimated to have started diverging prior to the initiation of glaciation, up to 3 Ma. These results add to a growing number of Southern Hemisphere examples of deep phylogeographic differentiation in glaciated alpine regions compared to Europe and North America, probably reflecting less intense glaciation. We suggest that other Southern Alps species showing northern and southern clades alone are more montane than alpine, and were reliant on warmer habitat to the north and south during glacial eras. Thus, there are species‐specific responses to climatic processes, influenced by distinctive habitat requirements and physiological traits.

Are Secondary Forests Ready for Climate Change? It Depends on Magnitude of Climate Change, Landscape Diversity and Ecosystem Legacies

In this review and synthesis paper, we review the resilience of secondary forests to climate change through the lenses of ecosystem legacies and landscape diversity. Ecosystem legacy of secondary forests was categorized as continuous forest, non-continuous forest, reassembled after conversion to other land uses, and novel reassembled forests of non-native species. Landscape diversity, including landforms that create varied local climatic and soil conditions, can buffer changing climate to some extent by allowing species from warmer climates to exist on warm microsites, while also providing refugial locations for species that grow in cool climates. We present five frames that allow forest managers to visualize a trajectory of change in the context of projected regional climate change, which are: Frame 1 (persistence), keep the same dominant tree species with little change; Frame 2 (moderate change), keep the same tree species with large changes in relative abundance; Frame 3 (forest biome change), major turnover in dominant tree species to a different forest biome; Frame 4 (forest loss), change from a forest to a non-forest biome; and Frame 5 (planted novel ecosystem), establish a novel ecosystem to maintain forest. These frames interact with ecosystem legacies and landscape diversity to determine levels of ecosystem resilience in a changing climate. Although forest readiness to adapt to Frame 1 and 2 scenarios, which would occur with reduced greenhouse gas emissions, is high, a business as usual climate change scenario would likely overwhelm the capacity of ecosystem legacies to buffer forest response, so that many forests would change to warmer forest biomes or non-forested biomes. Furthermore, the interactions among frames, legacies, and landscape diversity influence the transient dynamics of forest change; only Frame 1 leads to stable endpoints, while the other frames would have transient dynamics of change for the remainder of the 21st century.

Postglacial history of East European boreal forests in the mid‐Kama region, pre‐Urals, Russia

The Ural Mountains are an important climatic and biogeographical barrier between European and Siberian forests. In order to shed light on the postglacial formation and evolution of the boreal forests in the European pre‐Urals, we obtained a peat sediment core, Chernaya, from the Paltinskoe bog located between the southern taiga and hemiboreal forest zone in the mid‐Kama region. We carried out pollen analysis, non‐pollen palynomorph analysis, loss‐on‐ignition tests and radiocarbon dating. Radiocarbon dated records provide centennial to decennial resolution of the vegetation and environmental history of the European pre‐Urals for the last 8.8 ka. The postglacial formation of the pre‐Uralian hemiboreal forests reveals four important phases: (i) the dominance of Siberian taiga and forest‐steppe in the Early Holocene and beginning of the Middle Holocene (8.8–6.9 ka), indicating a dry climate; (ii) the spread of spruce and European broadleaved trees in the Middle Holocene (6.9–4 ka) under wetter climate conditions; (iii) the maximum extent of broadleaved trees coinciding with the arrival and spread of Siberian fir in the Late Holocene (4–2.3 ka); and (iv) the decline of broadleaved trees since the Early Iron Age (2.3 ka – present) possibly due to general climate cooling and logging. While temperate broadleaved trees possibly spread from local refugia in the Urals, fir arrived from Siberia and spread further west. The carbon accumulation rate of Paltinskoe bog (18.9±10.16 g C m−2 a−1) is close to the average value of carbon accumulation of northern peatlands. Local development of peat is characterized by non‐gradual growth with a phase of intensive carbon accumulation between 3.5 and 2.3 ka. The vegetation was strongly influenced by fire in the Early Holocene and by humans since the Early Iron Age practicing deforestation, agriculture and pasture. Phases of increased anthropogenic activity correlate well with the local archaeological data.

Genotyping-by-sequencing and ecological niche modeling illuminate phylogeography, admixture, and Pleistocene range dynamics in quaking aspen (Populus tremuloides).

Populus tremuloides is the widest‐ranging tree species in North America and an ecologically important component of mesic forest ecosystems displaced by the Pleistocene glaciations. Using phylogeographic analyses of genome‐wide SNPs (34,796 SNPs, 183 individuals) and ecological niche modeling, we inferred population structure, ploidy levels, admixture, and Pleistocene range dynamics of P. tremuloides, and tested several historical biogeographical hypotheses. We found three genetic lineages located mainly in coastal–Cascades (cluster 1), east‐slope Cascades–Sierra Nevadas–Northern Rockies (cluster 2), and U.S. Rocky Mountains through southern Canadian (cluster 3) regions of the P. tremuloides range, with tree graph relationships of the form ((cluster 1, cluster 2), cluster 3). Populations consisted mainly of diploids (86%) but also small numbers of triploids (12%) and tetraploids (1%), and ploidy did not adversely affect our genetic inferences. The main vector of admixture was from cluster 3 into cluster 2, with the admixture zone trending northwest through the Rocky Mountains along a recognized phenotypic cline (Utah to Idaho). Clusters 1 and 2 provided strong support for the “stable‐edge hypothesis” that unglaciated southwestern populations persisted in situ since the last glaciation. By contrast, despite a lack of clinal genetic variation, cluster 3 exhibited “trailing‐edge” dynamics from niche suitability predictions signifying complete northward postglacial expansion. Results were also consistent with the “inland dispersal hypothesis” predicting postglacial assembly of Pacific Northwestern forest ecosystems, but rejected the hypothesis that Pacific‐coastal populations were colonized during outburst flooding from glacial Lake Missoula. Overall, congruent patterns between our phylogeographic and ecological niche modeling results and fossil pollen data demonstrate complex mixtures of stable‐edge, refugial locations, and postglacial expansion within P. tremuloides. These findings confirm and refine previous genetic studies, while strongly supporting a distinct Pacific‐coastal genetic lineage of quaking aspen.

Genetic resources of relict populations of Pinus sylvestris (L.) in Western Carpathians assessed by chloroplast microsatellites

The relict character of the Scots pine populations from the Tatra Mts. (Western Carpathians) was formed on scarcely accessible, ecologically extreme habitats, in areas which were not under human activity. An exhaustive genetic analysis of the Scots pine populations from the refugial locations in the Tatra Mts. (Poland) had not yet been. In this study, we characterize the genetic variation and differentiation of the relict Scots pine populations from the Tatra Mts., to provide information on their genetic resources and the conservation implications. Eight paternally inherited chloroplast microsatellite loci were used to investigate the genetic structure of 4 relict populations, which were compared with the natural populations from the Baltic region (5 populations from Lithuania, Latvia and Estonia) and to a northern range from Russia (5 populations from the Kola Peninsula and Arkhangelsk Oblast). The four relict pine populations were characterized by a lower level of genetic variation when compared to the Baltic and northern populations, which was expressed in lower values of particular genetic parameters: numbers of alleles and haplotypes, haplotype genetic diversity, haplotype differentiation, and mean genetic distance between individuals in the population. Our results revealed a very high and significant genetic differentiation between all the analyzed populations, as well as between the three analyzed regions (PhiPT = 8%). Furthermore, the relict populations within a close geographic location showed higher differentiation (PhiPT = 5%) compared to the northern Russian and Baltic populations that were separated by tens and hundreds of kilometers. The relict populations of P. sylvestris from the Tatra Mts. deserve conservation efforts due to the fact that they are an important component if the species-poor Tatra forests.

Phylogeography of xerothermic Carlina acanthifolia subsp. utzka in Central Europe

Phylogeographic studies of grassland plants with broad Eurasian ranges point to the importance of northern refuges in shaping genetic patterns in populations across species distribution ranges in Central Europe. Carlina acanthifolia subsp. utzka is a common inhabitant of xerothermic sites in Central European dry grasslands. The aim of this study was to test hypotheses regarding some of the main phylogeographical patterns proposed for European grassland plants, in particular the locations of glacial refugia, the re-colonization routes, and genetic affinities between Southern, Eastern and Central European populations. We analyzed the genetic diversity of Carlina acanthifolia subsp. utzka based on distribution-wide sampling of 39 populations (Southern, Central and Eastern Europe) and compiled data obtained using different markers (AFLP, cpDNA, ETS region). The results for AFLP and the ETS region split the populations into two groups: from Central and Eastern Europe with the northern part of the Balkan Peninsula; and from its southern part. The segregation visible both in the distribution of particular haplotypes and in the variation level of the southern group of populations (AFLP) points to local processes that were taking place independently in the northern and the southern parts of the range. Populations from the southern part of the range have likely served as the core of the Central European part during their colonization, while re-colonization of glacial areas in Central Europe took place from local refugia in the central and western parts of Eastern Europe. The southern areas did not participate in this process. The observed variation of the frequency of haplotypes indicates that Eastern Europe populations dominant in the northern Balkan Peninsula got in contact with those from Central Europe. On the other hand, the presence of a separate line of haplotypes and ribotypes in populations from the southern part of the Balkan Peninsula indicates the absence of continuous connectivity of these areas with disjunct areas in Central Europe.

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 modeling using 27 EST-associated microsatellites. We also performed the species distribution modeling (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 the 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.

Mitochondrial DNA sequence data reveal the origins of postglacial marine macroalgal flora in the Northwest Atlantic

MEPS Marine Ecology Progress Series Contact the journal Facebook Twitter RSS Mailing List Subscribe to our mailing list via Mailchimp HomeLatest VolumeAbout the JournalEditorsTheme Sections MEPS 589:45-58 (2018) - DOI: https://doi.org/10.3354/meps12496 Mitochondrial DNA sequence data reveal the origins of postglacial marine macroalgal flora in the Northwest Atlantic Trevor T. Bringloe*, Gary W. Saunders Centre for Environmental and Molecular Algal Research (CEMAR), Department of Biology, University of New Brunswick, PO Box 4400, Fredericton, New Brunswick E3B 5A3, Canada *Corresponding author: trevor.bringloe@unb.ca ABSTRACT: Following the Last Glacial Maximum, the marine macroalgal flora in the Northwest (NW) Atlantic reportedly recolonized from Northeast (NE) Atlantic refugia. Genetic evidence for the few species tested, however, has indicated that some species survived glaciation in the NW Atlantic. Owing to the significant amount of data currently available, we sought to determine if COI-5P (5’ end of the cytochrome c oxidase subunit I gene) could distinguish between populations surviving glaciation on both sides of the Atlantic versus postglacial recolonization. COI-5P results were consistent with published findings using other markers in Chondrus crispus, Mastocarpus stellatus, Palmaria palmata, and Saccharina latissima. Having success, we then analyzed molecular data for several species of red and brown macroalgae to date isolation times between NE and NW Atlantic populations and determine what percentage of species survived in NW Atlantic refugia. We generated and gathered genetic data from COI-5P in 1560 specimens representing 20 amphi-Atlantic species, and estimated isolation times between NE and NW populations using calibrated red and brown COI-5P clocks in IMa2. Of the species surveyed, 60% had isolation time estimates between NE and NW Atlantic populations predating the Last Glacial Maximum. Recent shared ancestry was inferred in the remaining cases. Our results indicate that local refugia and/or trans-Arctic migration from the Pacific are the source populations for the majority of the NW Atlantic macroalgal flora. By shedding light on the phylogeographic history of the North Atlantic, we can better understand the nature of postglacial recolonization and forecast future changes to the NW Atlantic and Canadian Arctic. KEY WORDS: COI-5P · Glacial refugia · Macroalgae · North Atlantic · IMa2 · Last Glacial Maximum · Seaweed Full text in pdf format Supplementary material Correction PreviousNextCite this article as: Bringloe TT, Saunders GW (2018) Mitochondrial DNA sequence data reveal the origins of postglacial marine macroalgal flora in the Northwest Atlantic. Mar Ecol Prog Ser 589:45-58. https://doi.org/10.3354/meps12496 Export citation RSS - Facebook - Tweet - linkedIn Cited by Published in MEPS Vol. 589. Online publication date: February 23, 2018 Print ISSN: 0171-8630; Online ISSN: 1616-1599 Copyright © 2018 Inter-Research.

Population genetic structure of the endemic rosewoods Dalbergia cochinchinensis and D.oliveri at a regional scale reflects the Indochinese landscape and life-history traits.

Indochina is a biodiversity hot spot and harbors a high number of endemic species, most of which are poorly studied. This study explores the genetic structure and reproductive system of the threatened endemic timber species Dalbergia cochinchinensis and Dalbergia oliveri using microsatellite data from populations across Indochina and relates it to landscape characteristics and life‐history traits. We found that the major water bodies in the region, Mekong and Tonle Sap, represented barriers to gene flow and that higher levels of genetic diversity were found in populations in the center of the distribution area, particularly in Cambodia. We suggest that this pattern is ancient, reflecting the demographic history of the species and possible location of refugia during earlier time periods with limited forest cover, which was supported by signs of old genetic bottlenecks. The D. oliveri populations had generally high levels of genetic diversity (mean H e = 0.73), but also strong genetic differentiation among populations (global GST = 0.13), while D. cochinchinensis had a moderate level of genetic diversity (mean H e = 0.55), and an even stronger level of differentiation (global GST = 0.25). These differences in genetic structure can be accounted for by a higher level of gene flow in D. oliveri due to a higher dispersal capacity, but also by the broader distribution area for D. oliveri, and the pioneer characteristics of D. cochinchinensis. This study represents the first detailed analysis of landscape genetics for tree species in Indochina, and the found patterns might be common for other species with similar ecology.

Evolutionary history of enigmatic bears in the Tibetan Plateau-Himalaya region and the identity of the yeti.

Although anecdotally associated with local bears (Ursus arctos and U. thibetanus), the exact identity of ‘hominid’-like creatures important to folklore and mythology in the Tibetan Plateau–Himalaya region is still surrounded by mystery. Recently, two purported yeti samples from the Himalayas showed genetic affinity with an ancient polar bear, suggesting they may be from previously unrecognized, possibly hybrid, bear species, but this preliminary finding has been under question. We conducted a comprehensive genetic survey of field-collected and museum specimens to explore their identity and ultimately infer the evolutionary history of bears in the region. Phylogenetic analyses of mitochondrial DNA sequences determined clade affinities of the purported yeti samples in this study, strongly supporting the biological basis of the yeti legend to be local, extant bears. Complete mitochondrial genomes were assembled for Himalayan brown bear (U. a. isabellinus) and black bear (U. t. laniger) for the first time. Our results demonstrate that the Himalayan brown bear is one of the first-branching clades within the brown bear lineage, while Tibetan brown bears diverged much later. The estimated times of divergence of the Tibetan Plateau and Himalayan bear lineages overlap with Middle to Late Pleistocene glaciation events, suggesting that extant bears in the region are likely descendants of populations that survived in local refugia during the Pleistocene glaciations.

Multilocus genetic analyses and spatial modeling reveal complex population structure and history in a widespread resident North American passerine (Perisoreus canadensis).

An increasing body of studies of widely distributed, high latitude species shows a variety of refugial locations and population genetic patterns. We examined the effects of glaciations and dispersal barriers on the population genetic patterns of a widely distributed, high latitude, resident corvid, the gray jay (Perisoreus canadensis), using the highly variable mitochondrial DNA (mtDNA) control region and microsatellite markers combined with species distribution modeling. We sequenced 914 bp of mtDNA control region for 375 individuals from 37 populations and screened seven loci for 402 individuals from 27 populations across the gray jay range. We used species distribution modeling and a range of phylogeographic analyses (haplotype diversity, ΦST, SAMOVA, F ST, Bayesian clustering analyses) to examine evolutionary history and population genetic structure. MtDNA and microsatellite markers revealed significant genetic differentiation among populations with high concordance between markers. Paleodistribution models supported at least five potential areas of suitable gray jay habitat during the last glacial maximum and revealed distributions similar to the gray jay's contemporary during the last interglacial. Colonization from and prolonged isolation in multiple refugia is evident. Historical climatic fluctuations, the presence of multiple dispersal barriers, and highly restricted gene flow appear to be responsible for strong genetic diversification and differentiation in gray jays.