Complex fine‐scale phylogeographical patterns in a putative refugial region for Fagus sylvatica (Fagaceae)

Broad‐scale plastid (chloroplast) DNA studies of beech (Fagus sylvatica) populations suggest the existence of glacial refugia and introgression zones in south‐eastern Europe. We choose a possible refugium of beech in northern Greece, Mt. Paggeo, which hosts a private plastid haplotype for beech, to conduct a fine‐scale genetic study. We attempt to confirm or reject the hypothesis of the existence of a small‐scale refugium and to gain an understanding of the ecological and topographical factors affecting the spatial distribution of plastid haplotypes in the area. Our results reveal a high haplotype diversity on Mt. Paggeo, but the overall distribution of haplotypes shows no significant correlation with the ecological characteristics of the beech forests. However, the private haplotype is found at high frequencies in beech forests located in or near ravines, having a high spatial overlap with a relict vegetation type occurring in ecological conditions found mainly in ravines. This result emphasizes the importance of topography in the existence of glacial refugia in the wider area. Furthermore, haplotypes originating from two more widespread beech lineages in Greece are found on Mt. Paggeo, indicating a possible mixing of populations originating from a local refugium with populations from remote refugia that possibly migrated into the area after the last glaciation. © 2014 The Linnean Society of London, Botanical Journal of the Linnean Society, 2014, 174 , 516–528.     

Highest drought sensitivity and lowest resistance to growth suppression are found in the range core of the tree Fagus sylvatica L. not the equatorial range edge

Biogeographical and ecological theory suggests that species distributions should be driven to higher altitudes and latitudes as global temperatures rise. Such changes occur as growth improves at the poleward edge of a species distribution and declines at the range edge in the opposite or equatorial direction, mirrored by changes in the establishment of new individuals. A substantial body of evidence demonstrates that such processes are underway for a wide variety of species. Case studies from populations at the equatorial range edge of a variety of woody species have led us to understand that widespread growth decline and distributional shifts are underway. However, in apparent contrast, other studies report high productivity and reproduction in some range edge populations. We sought to assess temporal trends in the growth of the widespread European beech tree (Fagus sylvatica) across its latitudinal range. We explored the stability of populations to major drought events and the implications for predicted widespread growth decline at its equatorial range edge. In contrast to expectations, we found greatest sensitivity and low resistance to drought in the core of the species range, whilst dry range edge populations showed particularly high resistance to drought and little evidence of drought‐linked growth decline. We hypothesize that this high range edge resistance to drought is driven primarily by local environmental factors that allow relict populations to persist despite regionally unfavourable climate. The persistence of such populations demonstrates that range‐edge decline is not ubiquitous and is likely to be driven by declining population density at the landscape scale rather than sudden and widespread range retraction.     

Reconstruction of the colonization route from glacial refugium to the northern distribution range of the European butterfly Polyommatus coridon (Lepidoptera: Lycaenidae)

Genetic analyses are useful tools for reconstructing glacial distribution patterns and postglacial expansion corridors. However, little information is available about the latter. We reconstruct the expansion corridors of the butterfly Polyommatus coridon from its glacial refugium to the northern edge of its current distribution by comparing populations from southern Lower Saxony (central Germany) to other existing genetic data sets. The populations from Lower Saxony clearly belonged to a western lineage that expanded postglacially from the Adriatic‐Mediterranean region. They form part of a southern German group passing through the Burgundian Gap. In the southern German group, populations belong to a western subgroup. Therefore, expansion followed the Rhine valley and through Hesse, finally reaching southern Lower Saxony and western Thuringia in central Germany. Thus, we present a complete colonization route from the glacial refugium to the northern distribution range of P. coridon. Such data are useful for understanding the biogeographic structure and migration corridors for other mobile Mediterranean species.     

Low genetic diversity in small leading edge populations of the European paleoendemic Ramonda serbica (Gesneriaceae) in Bulgaria

Ramonda serbica Pan?. (Gesneriaceae) is an endangered endemic species of the Balkan Peninsula which has been the subject of several studies in the past, but has not yet been investigated in terms of its genetic variation. Ramonda serbica is one of only five European representatives of the mainly subtropical family Gesneriaceae categorized as paleoendemics or Tertiary relicts sequestered in southern Europe by Quaternary climate oscillations. Here, an inter simple sequence repeat (ISSR) analysis was performed to determine the genetic diversity of five populations sampled from the geographically eastern fringe of its range in northwestern Bulgaria. We found relatively low levels of genetic diversity and significant genetic differentiation among the investigated populations, typical of a leading edge scenario. From a conservation point of view, the low genetic diversity, together with the presence of only few extant localities stress the need for urgent in situ and ex situ conservation actions to ensure the long‐term survival of R. serbica in Bulgaria.     

History vs. habitat type: explaining the genetic structure of European nine‐spined stickleback (Pungitius pungitius) populations

The genetic structure of contemporary populations can be shaped by both their history and current ecological conditions. We assessed the relative importance of postglacial colonization history and habitat type in the patterns and degree of genetic diversity and differentiation in northern European nine‐spined sticklebacks (Pungitius pungitius), using mitochondrial DNA (mtDNA) sequences and 12 nuclear microsatellite and insertion/deletion loci. The mtDNA analyses identified – and microsatellite analyses supported – the existence of two historically distinct lineages (eastern and western). The analyses of nuclear loci among 51 European sites revealed clear historically influenced and to minor degree habitat dependent, patterns of genetic diversity and differentiation. While the effect of habitat type on the levels of genetic variation (coastal > freshwater) and differentiation (freshwater > coastal) was clear, the levels of genetic variability and differentiation in the freshwater sites were independent of habitat type (viz. river, lake and pond). However, levels of genetic variability, together with estimates of historical effective population sizes, decreased dramatically and linearly with increasing latitude. These geographical patterns of genetic variability and differentiation suggest that the contemporary genetic structure of freshwater nine‐spined sticklebacks has been strongly impacted by the founder events associated with postglacial colonization and less by current ecological conditions (cf. habitat type). In general, the results highlight the strong and persistent effects of postglacial colonization history on genetic structuring of northern European fauna and provide an unparalleled example of latitudinal trends in levels of genetic diversity.     

Long‐term ‘islands’ in the landscape: low gene flow,effective population size and genetic divergence in the shrub Hakea oldfieldii (Proteaceae)

The genetic structure of disjunct populations is determined by founding genetic properties, demographic processes, gene flow, drift and local selection. We aim to identify the genetic consequences of natural population disjunction at regional and local scales in Hakea oldfieldii using nuclear and plastid markers to investigate long‐term effective population sizes and gene flow, and patterns of diversity and divergence, among populations. Regional divergence was significant as shown by a consistent pattern in principal coordinates, neighbor‐joining and Bayesian analyses, but divergence at the local level was also significant with localized distribution of plastid haplotypes and populations clustering separately in Bayesian analyses. Historical, recent and first‐generation gene flow was low, suggesting that recent habitat fragmentation has not reduced gene migration significantly. Genetic bottlenecks were detected in three populations. Long‐term effective population size was significantly correlated with the number of alleles/locus and observed heterozygosity, but not with census population size, suggesting that the loss of diversity is associated with long‐term changes rather than recent fragmentation. Inbreeding coefficients were significant in only three populations, suggesting that the loss of diversity is linked to drift and bottlenecks associated with demographic processes (local extinction by fires) rather than inbreeding. Historical disjunction as a result of specific ecological requirements, contraction of habitats following drying during the Pleistocene, low gene flow and changes in population size are likely to have been important forces driving divergence through isolation by distance and drift. © 2015 The Linnean Society of London, Botanical Journal of the Linnean Society, 2015, 179 , 319–334.     

No obvious genetic erosion,but evident relict status at the westernmost range edge of the Pontic‐Pannonian steppe plant Linum flavum L. (Linaceae) in Central Europe

We investigate patterns of genetic variation along an east–west transect of Central European populations of Linum flavum and interpret the Quaternary history of its peripheral populations, especially those at the westernmost isolated range edge, discussing their migrations and possible relict status. We defined our peripheral transect across three study regions from Central Hungary, eastern Austria to southwestern Germany. Using AFLP fingerprinting and cpDNA sequence variation (rpL16 intron, atpI‐H), we analyzed 267 and 95 individuals, respectively, representing each study region by four populations. Hierarchical AMOVA (AFLPs) indicated significant variation among study regions (12% of total variance) and moderate differentiation between populations (10%). Population differentiation was high at the westernmost range edge (11.5%, Germany), but also in the east (13.4%, Hungary), compared to the Austrian study region (8.6%). Correspondingly, AFLP diversity was highest in the center of the study transect in eastern Austria. CpDNA haplotypes support a pattern of regional structuring with the strongest separation of the westernmost range edge, and some haplotype sharing among Austrian and Hungarian individuals. Equilibrating nucleotide versus haplotype diversity patterns, the highly diverse populations at the Pannonian range edge (Austria) indicate long‐term persistence, while Central Pannonian populations are obviously effected by recent bottlenecks. Intermediate nucleotide, but high haplotype diversity within the westernmost exclave (Swabian Alb), is indicative of a founder bottleneck during its pre‐LGM or early postglacial migration history, followed by sufficient time to accumulate cpDNA variation. The not obviously reduced genetic diversity and distinctiveness of L. flavum at the westernmost range edge suggest a long‐term persistence (relict status) of populations in this region, where the species has survived probably even the Würm glaciation in extra‐Mediterranean refugia. This genetic relict variation represents an important part of the overall genetic diversity found in the western periphery of this steppe plant and highlights the high conservation priority of respective gene pools.     

Avian ecological succession in the Amazon: A long‐term case study following experimental deforestation

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Variation in fine root biomass of three European tree species: Beech (Fagus sylvatica L.), Norway spruce (Picea abies L. Karst.), and Scots pine (Pinus sylvestris L.)

Abstract

Fine roots (<2 mm) are very dynamic and play a key role in forest ecosystem carbon and nutrient cycling and accumulation. We reviewed root biomass data of three main European tree species European beech, (Fagus sylvatica L.), Norway spruce (Picea abies L. Karst.) and Scots pine (Pinus sylvestris L.), in order to identify the differences between species, and within and between vegetation zones, and to show the relationships between root biomass and the climatic, site and stand factors. The collected literature consisted of data from 36 beech, 71 spruce and 43 pine stands. The mean fine root biomass of beech was 389 g m^?2, and that of spruce and pine 297 g m^?2 and 277 g m^?2, respectively. Data from pine stands supported the hypothesis that root biomass is higher in the temperate than in the boreal zone. The results indicated that the root biomass of deciduous trees is higher than that of conifers. The correlations between root biomass and site fertility characteristics seemed to be species specific. There was no correlation between soil acidity and root biomass. Beech fine root biomass decreased with stand age whereas pine root biomass increased with stand age. Fine root biomass at tree level correlated better than stand level root biomass with stand characteristics. The results showed that there exists a strong relationship between the fine root biomass and the above-ground biomass.     

The genetic structure of the steppe plant Iris aphylla L. at the northern limit of its geographical range

Genetic diversity of Iris aphylla was examined in seven Polish populations located at the northern limit of the geographical range of the species. Using RAPD analysis, 491 DNA fragments were amplified, all of which were polymorphic. The peripheral populations were characterized by a low number of unique bands (one to three per population) and moderate values of genetic diversity parameters (percent of polymorphic loci = 30.6%, Shannon's index = 0.149 and Nei's gene diversity = 0.097, on average), which can be explained as being due to the recent expansion of the European biota and the extremely low frequency or absence of seed set and of juveniles, as well as limited pollen and seed dispersal. There was also no significant correlation between ecological properties (population size; number of flowering ramets and fruits) and genetic diversity parameters. Despite this fact, more fixed loci were noted in the smallest populations than were in the largest ones. All populations were significantly differentiated and geographically structured. Analysis of molecular variance between regions showed a low and nonsignificant value, but relatively high molecular variation was partitioned among and within populations. Only one group of south-eastern populations was structured according to isolation by distance pattern and neighbour-joining cluster analysis. © 2006 The Linnean Society of London, Botanical Journal of the Linnean Society , 2006, 152 , 245–255.     

Genetic consequences of fragmentation in “arbor vitae,” eastern white cedar (Thuja occidentalis L.), toward the northern limit of its distribution range

We tested the hypothesis that marginal fragmented populations of eastern white cedar (EWC) are genetically isolated due to reduced pollen and gene flow. In accordance with the central-marginal model, we predicted a decrease in population genetic diversity and an increase in differentiation along the latitudinal gradient from the boreal mixed-wood to northern coniferous forest. A total of 24 eastern white cedar populations were sampled along the north-south latitudinal gradient for microsatellite genotyping analysis. Positive F_is values and heterozygote deficiency were observed in populations from the marginal (F_is = 0.244; P_HW = 0.0042) and discontinuous zones (F_is = 0.166; P_HW = 0.0042). However, populations from the continuous zone were in HW equilibrium (F_is = −0.007; P_HW = 0.3625). There were no significant latitudinal effects on gene diversity (H_s), allelic richness (AR), or population differentiation (F_st). Bayesian and NJT (neighbor-joining tree) analyses demonstrated the presence of a population structure that was partly consistent with the geographic origins of the populations. The impact of population fragmentation on the genetic structure of EWC is to create a positive inbreeding coefficient, which was two to three times higher on average than that of a population from the continuous zone. This result indicated a higher occurrence of selfing within fragmented EWC populations coupled with a higher degree of gene exchange among near-neighbor relatives, thereby leading to significant inbreeding. Increased population isolation was apparently not correlated with a detectable effect on genetic diversity. Overall, the fragmented populations of EWC appear well-buffered against effects of inbreeding on genetic erosion.     

Spangled perch (Leiopotherapon unicolor) in the southern Murray‐Darling Basin: Flood dispersal and short‐term persistence outside its core range

The spangled perch Leiopotherapon unicolor is considered a rare vagrant in the southern Murray‐Darling Basin, Australia, due to its intolerance of the relatively cool water temperatures that prevail during winter months. This study details 1342 records of the species from 68 locations between 2010 and 2014 outside its accepted ‘core adult range’ following widespread flooding during 2010 and 2011. Although records of the species declined over 2013, L. unicolor remained resident in the southern Murray‐Darling Basin as of April 2014. The species persisted in several locations for three consecutive winters with recruitment documented at two sites. This study represents the first identification of the dispersal of large numbers of L. unicolor into the southern Murray‐Darling Basin, persistence beyond a single winter, and recruitment by the species in habitats south of its recognized ‘core adult range’. Targeted research would determine the potential for predicted environmental changes (artificially warmer drainage wetlands, climate change and greater floodplain connectivity) to facilitate longer term persistence and range expansion by the species in the southern Murray‐Darling Basin.     

Inferring selection in instances of long‐range colonization: The Aleppo pine (Pinus halepensis) in the Mediterranean Basin

Teasing apart the effects of natural selection and demography on current allele frequencies is challenging, due to both processes leaving a similar molecular footprint. In particular, when attempting to identify selection in species that have undergone a recent range expansion, the increase in genetic drift at the edges of range expansions (“allele surfing”) can be a confounding factor. To address this potential issue, we first assess the long‐range colonization history of the Aleppo pine across the Mediterranean Basin, using molecular markers. We then look for single nucleotide polymorphisms (SNPs) involved in local adaptation using: (a) environmental correlation methods (bayenv2 ), focusing on bioclimatic variables important for the species’ adaptation (i.e., temperature, precipitation and water availability); and (b) F_ST‐related methods (pcadapt ). To assess the rate of false positives caused by the allele surfing effect, these results are compared with results from simulated SNP data that mimics the species’ past range expansions and the effect of genetic drift, but with no selection. We find that the Aleppo pine shows a previously unsuspected complex genetic structure across its range, as well as evidence of selection acting on SNPs involved with the response to bioclimatic variables such as drought. This study uses an original approach to disentangle the confounding effects of drift and selection in range margin populations. It also contributes to the increased evidence that plant populations are able to adapt to new environments despite the expected accumulation of deleterious mutations that takes place during long‐range colonizations.     

Evidence for long‐term migration on the Balkan Peninsula using dental and cranial nonmetric data: Early interaction between Corinth (Greece) and its colony at Apollonia (Albania)

This article seeks to identify “Greeks” and “non‐Greeks” in “mixed” mortuary contexts in a Greek colony. Specifically, we test the hypothesis that Illyrian and Greek individuals lived and were buried together at the Corinthian colony of Apollonia, Albania (established ca. 600 BC). The pattern of human biological interaction at Apollonia is tested by identifying variation in genetic relatedness using biodistance analysis of dental and cranial nonmetric traits for three sites: Apollonia (n = 116), its founder‐city Corinth (n = 69), and Lofkënd (n = 108), an inland site near Apollonia pre‐dating colonization. Logistic regression analysis estimates that individuals from colonial Apollonia are most closely related to prehistoric Illyrian populations (from Lofkënd and prehistoric Apollonia), rather than Greeks (from Corinth). The phenotypic similarity between colonial Apollonia and prehistoric Illyria suggests that there was a large Illyrian contribution to the gene pool at the colony of Apollonia. However, some trait combinations show low biological distances among all groups, suggesting homogeneity among Illyrian and Greek populations (assessed through pseudo‐Mahalanobis' D²). The degree of phenotypic similarity suggests shared ancestry and long‐term migration throughout these regions. The impacts of missing data and small sample sizes are also considered. Am J Phys Anthropol 153:236–248, 2014. © 2013 Wiley Periodicals, Inc.     

Genetic structure at range edge: low diversity and high inbreeding in Southeast Asian mangrove (Avicennia marina) populations

Understanding the genetic composition and mating systems of edge populations provides important insights into the environmental and demographic factors shaping species' distribution ranges. We analysed samples of the mangrove Avicennia marina from Vietnam, northern Philippines and Australia, with microsatellite markers. We compared genetic diversity and structure in edge (Southeast Asia, and Southern Australia) and core (North and Eastern Australia) populations, and also compared our results with previously published data from core and southern edge populations. Comparisons highlighted significantly reduced gene diversity and higher genetic structure in both margins compared to core populations, which can be attributed to very low effective population size, pollinator scarcity and high environmental pressure at distribution margins. The estimated level of inbreeding was significantly higher in northeastern populations compared to core and southern populations. This suggests that despite the high genetic load usually associated with inbreeding, inbreeding or even selfing may be advantageous in margin habitats due to the possible advantages of reproductive assurance, or local adaptation. The very high level of genetic structure and inbreeding show that populations of A. marina are functioning as independent evolutionary units more than as components of a metapopulation system connected by gene flow. The combinations of those characteristics make these peripheral populations likely to develop local adaptations and therefore to be of particular interest for conservation strategies as well as for adaptation to possible future environmental changes.     

Long‐term metapopulation study of the Glanville fritillary butterfly (Melitaea cinxia): survey methods,data management,and long‐term population trends

Long‐term observational studies conducted at large (regional) spatial scales contribute to better understanding of landscape effects on population and evolutionary dynamics, including the conditions that affect long‐term viability of species, but large‐scale studies are expensive and logistically challenging to keep running for a long time. Here, we describe the long‐term metapopulation study of the Glanville fritillary butterfly (Melitaea cinxia) that has been conducted since 1991 in a large network of 4000 habitat patches (dry meadows) within a study area of 50 by 70 km in the Åland Islands in Finland. We explain how the landscape structure has been described, including definition, delimitation, and mapping of the habitat patches; methods of field survey, including the logistics, cost, and reliability of the survey; and data management using the EarthCape biodiversity platform. We describe the long‐term metapopulation dynamics of the Glanville fritillary based on the survey. There has been no long‐term change in the overall size of the metapopulation, but the level of spatial synchrony and hence the amplitude of fluctuations in year‐to‐year metapopulation dynamics have increased over the years, possibly due to increasing frequency of exceptional weather conditions. We discuss the added value of large‐scale and long‐term population studies, but also emphasize the need to integrate more targeted experimental studies in the context of long‐term observational studies. For instance, in the case of the Glanville fritillary project, the long‐term study has produced an opportunity to sample individuals for experiments from local populations with a known demographic history. These studies have demonstrated striking differences in dispersal rate and other life‐history traits of individuals from newly established local populations (the offspring of colonizers) versus individuals from old, established local populations. The long‐term observational study has stimulated the development of metapopulation models and provided an opportunity to test model predictions. This combination of empirical studies and modeling has facilitated the study of key phenomena in spatial dynamics, such as extinction threshold and extinction debt.     

Genetic homogeneity of the Sedgling Nehalennia speciosa (Odonata: Coenagrionidae) indicates a single Würm glacial refugium and trans‐Palaearctic postglacial expansion

The phylogeographic structures of taiga species often support the hypothesis of East Palaearctic refugia for these taxa, but the phylogeographic structures of northern temperate and southern boreal bog species are still poorly understood. Therefore, we analysed the genetic diversity and differentiation of a stenotopic damselfly, Nehalennia speciosa, across its trans‐Palaearctic range by means of sequencing two mitochondrial gene fragments, 16S rRNA‐ND1 and cytochrome c oxidase II. Only four single nucleotide polymorphisms were detected over the 1130 sequenced nucleotides. This low genetic diversity and differentiation and thus the lack of phylogeographic structure imply postglacial expansion from a single Würm Ice Age refugium, most likely located in the Far East of Asia, i.e. Manchurian refugium. From here, the species could have colonized large parts of the Palaearctics, including Europe, during the postglacial.     

Genetic Variation in Fragmented Forest Stands of the Andean Oak Quercus humboldtii Bonpl. (Fagaceae)1

Quercus humboldtii is a montane forest dominant species in Colombia, which has experienced significant habitat loss. Using three microsatellite loci, we compared the genetic diversity of adults and seedlings in fragments of small and large size. Results show high genetic diversity, comparable to other temperate oak species (H_o= 0.813, H_e= 0.780, and f=?0.044). However, allelic richness reduction in seedlings of the most fragmented part of the landscape, suggested restricted gene flow and risk of future genetic bottlenecks, if larger tracts of forest disappear.     

The effect of deforestation on the genetic diversity and structure in <Emphasis Type="Italic">Acer saccharum</Emphasis> (Marsh): Evidence for the loss and restructuring of genetic variation in a natural system

The level and distribution of genetic diversity can be influenced by species life history traits and demographic factors, including perturbations that might produce population bottlenecks. Deforestation and forest fragmentation are common sources of population disturbance in contemporary populations of forest ecosystems. Although the genetic effects of forest fragmentation and deforestation have been examined by assessing levels of genetic variation in forest fragments that remain after logging, few considerations have been made of the populations that re-colonize once-cleared areas. Here we examine the effects of human-mediated population bottlenecks on the level and distribution of genetic diversity in natural populations of the long-lived forest tree species, Acer saccharum (sugar maple). We compared genetic variation and structure for populations of sugar maple found within old-growth forested area and in area that has re-colonized since logging. In this study the percent polymorphic loci and allelic richness estimates were reduced in the logged populations compared to old-growth populations. Jackknifed estimates of population genetic differentiation showed significantly higher differentiation among logged populations, with this result being consistently seen when individuals within populations were grouped according to diameter at breast height. The result of decreased genetic variation and higher levels of genetic structure among logged populations suggests that even one extensive bout of logging can alter the level and distribution of genetic variation in this forest tree species.