Refugia revisited: individualistic responses of species in space and time

Genetic evidence for glacial refugia of the temperate tree Eucryphia cordifolia (Cunoniaceae) in southern South America

PREMISE OF THE STUDY

The temperate forests of southern South America were greatly affected by glaciations. Previous studies have indicated that some cold-tolerant tree species were able to survive glacial periods in small, ice-free patches within glaciated areas in the Andes and in southern Patagonia. Here we asked whether populations of the mesothermic species Eucryphia cordifolia also were able to survive glaciations in these areas or only in unglaciated coastal areas.

METHODS

The chloroplast intergenic spacer trnV-ndhC was sequenced for 150 individuals from 22 locations. Genetic data were analyzed (standard indexes of genetic diversity, a haplotype network, and genetic differentiation) in a geographical context.

KEY RESULTS

Two of the nine haplotypes detected were widespread in high frequency across the entire range of the species. The highest levels of genetic diversity were found around 40°S, decreasing sharply northward and more moderately southward. No differences in genetic diversity were found between Andean and coastal populations. Notably, seven haplotypes were found in a small area of the Coast Range known as the Cordillera Pelada (40°S). The differentiation coefficients G(ST) and N(ST) revealed that most of the genetic variation detected was due to variation within populations.

CONCLUSIONS

The low levels of population differentiation and the high genetic diversity found in the Cordillera Pelada suggest that this area was the main refugium for E. cordifolia during glaciations. Nevertheless, given the high levels of genetic diversity found in some Andean populations, we cannot discount that some local populations also survived the glaciation in the Andes.

Comparative phylogeography in a specific and obligate pollination antagonism

In specific and obligate interactions the nature and abundance of a given species can have important effects on the survival and population dynamics of associated organisms. In a phylogeographic framework, we therefore expect that the fates of organisms interacting specifically are also tightly interrelated. Here we investigate such a scenario by analyzing the genetic structures of species interacting in an obligate plant-insect pollination lure-and-trap antagonism, involving Arum maculatum (Araceae) and its specific psychodid (Diptera) visitors Psychoda phalaenoides and Psycha grisescens. Because the interaction is asymmetric (i.e., only the plant depends on the insect), we expect the genetic structure of the plant to be related with the historical pollinator availability, yielding incongruent phylogeographic patterns between the interacting organisms.Using insect mtDNA sequences and plant AFLP genome fingerprinting, we inferred the large-scale phylogeographies of each species and the distribution of genetic diversities throughout the sampled range, and evaluated the congruence in their respective genetic structures using hierarchical analyses of molecular variances (AMOVA). Because the composition of pollinator species varies in Europe, we also examined its association with the spatial genetic structure of the plant.Our findings indicate that while the plant presents a spatially well-defined genetic structure, this is not the case in the insects. Patterns of genetic diversities also show dissimilar distributions among the three interacting species. Phylogeographic histories of the plant and its pollinating insects are thus not congruent, a result that would indicate that plant and insect lineages do not share the same glacial and postglacial histories. However, the genetic structure of the plant can, at least partially, be explained by the type of pollinators available at a regional scale. Differences in life-history traits of available pollinators might therefore have influenced the genetic structure of the plant, the dependent organism, in this antagonistic interaction.

Demographic history, genetic structure and gene flow in a steppe-associated raptor species

Background

Environmental preferences and past climatic changes may determine the length of time during which a species range has contracted or expanded from refugia, thereby influencing levels of genetic diversification. Connectivity among populations of steppe-associated taxa might have been maximal during the long glacial periods, and interrupted only during the shorter interglacial phases, potentially resulting in low levels of genetic differentiation among populations. We investigated this hypothesis by exploring patterns of genetic diversity, past demography and gene flow in a raptor species characteristic of steppes, the Montagu's harrier (Circus pygargus), using mitochondrial DNA data from 13 breeding populations and two wintering populations.

Results

Consistent with our hypothesis, Montagu's harrier has relatively low genetic variation at the mitochondrial DNA. The highest levels of genetic diversity were found in coastal Spain, France and central Asia. These areas, which were open landscapes during the Holocene, may have acted as refugia when most of the European continent was covered by forests. We found significant genetic differentiation between two population groups, at the SW and NE parts of the species' range. Two events of past population growth were detected, and occurred ca. 7500-5500 and ca. 3500-1000 years BP in the SW and NE part of the range respectively. These events were likely associated with vegetation shifts caused by climate and human-induced changes during the Holocene.

Conclusions

The relative genetic homogeneity observed across populations of this steppe raptor may be explained by a short isolation time, relatively recent population expansions and a relaxed philopatry. We highlight the importance of considering the consequence of isolation and colonization processes in order to better understand the evolutionary history of steppe species.

Faunal histories from Holocene ancient DNA

Recent studies using ancient DNA have been instrumental in advancing understanding of the impact of Holocene climate change on biodiversity. Ancient DNA has been used to track demography, migration and diversity, and is providing new insights into the long-term dynamics of species and population distributions. The Holocene is key to understanding how the past has impacted on the present, as it bridges the gap between contemporary phylogeographic studies and those with inference on Pleistocene patterns, based on ancient DNA studies. Here, we examine the major patterns of Holocene faunal population dynamics and connectivity; highlighting the dynamic nature of species and population responses to Holocene climatic change, thereby providing an 'analogue' for understanding potential impacts of future change.

Consequences of range contractions and range shifts on molecular diversity

Due to past and current climatic changes, range contractions and range shifts are essential stages in the history of a species. However, unlike range expansions, the molecular consequences of these processes have been little investigated. In order to fill this gap, we simulated patterns of molecular diversity within and between populations for various types of range contractions and range shifts. We show that range contractions tend to decrease genetic diversity as compared with population with stable ranges but quite counterintuitively fast range contractions preserve higher levels of diversity and induce lower levels of genetic differentiation among refuge areas than slow contractions. Contrastingly, fast range shifts lead to lower levels of diversity than slow range shifts. At odds with our expectations, we find that species actively migrating toward refuge areas can only preserve higher levels of diversity in refugia if the contraction is rapid. Under slow range contraction or slow range shift, active migration toward refugia lead to a larger loss of diversity as compared with scenarios with isotropic migration and may thus not be a good evolutionary strategy. These results suggest that the levels of diversity preserved after a climate change both within and between refuge areas will not only depend on the dispersal abilities of a species but also on the speed of the change. It also implies that a given episode of climatic change will impact differently species with different generation times.

Modern and ancient red fox (Vulpes vulpes) in Europe show an unusual lack of geographical and temporal structuring, and differing responses within the carnivores to historical climatic change

Background

Despite phylogeographical patterns being well characterised in a large number of species, and generalised patterns emerging, the carnivores do not all appear to show consistent trends. While some species tend to fit with standard theoretical phylogeographic expectations (e.g. bears), others show little obvious modern phylogeographic structure (e.g. wolves). In this study we briefly review these studies, and present a new phylogeographical study of the red fox (Vulpes vulpes) throughout Europe, using a combination of ancient DNA sequences obtained from museum specimens, and modern sequences collated from GenBank. We used cytochrome b (250 bp) and the mitochondrial control region (268 bp) to elucidate both current and historical phylogeographical patterning.

Results

We found evidence for slight isolation by distance in modern populations, as well as differentiation associated with time, both of which can likely be attributed to random genetic drift. Despite high sequence diversity (11.2% cytochrome b, 16.4% control region), no evidence for spatial structure (from Bayesian trees) is found either in modern samples or ancient samples for either gene, and Bayesian skyline plots suggested little change in the effective population size over the past 40,000 years.

Conclusions

It is probable that the high dispersal ability and adaptability of the red fox has contributed to the lack of observable differentiation, which appears to have remained consistent over tens of thousands of years. Generalised patterns of how animals are thought to have responded to historical climatic change are not necessarily valid for all species, and so understanding the differences between species will be critical for predicting how species will be affected by future climatic change.

Ancient hybridization and an Irish origin for the modern polar bear matriline

BACKGROUND

Polar bears (Ursus maritimus) are among those species most susceptible to the rapidly changing arctic climate, and their survival is of global concern. Despite this, little is known about polar bear species history. Future conservation strategies would significantly benefit from an understanding of basic evolutionary information, such as the timing and conditions of their initial divergence from brown bears (U. arctos) or their response to previous environmental change.

RESULTS

We used a spatially explicit phylogeographic model to estimate the dynamics of 242 brown bear and polar bear matrilines sampled throughout the last 120,000 years and across their present and past geographic ranges. Our results show that the present distribution of these matrilines was shaped by a combination of regional stability and rapid, long-distance dispersal from ice-age refugia. In addition, hybridization between polar bears and brown bears may have occurred multiple times throughout the Late Pleistocene.

CONCLUSIONS

The reconstructed matrilineal history of brown and polar bears has two striking features. First, it is punctuated by dramatic and discrete climate-driven dispersal events. Second, opportunistic mating between these two species as their ranges overlapped has left a strong genetic imprint. In particular, a likely genetic exchange with extinct Irish brown bears forms the origin of the modern polar bear matriline. This suggests that interspecific hybridization not only may be more common than previously considered but may be a mechanism by which species deal with marginal habitats during periods of environmental deterioration.

A Holarctic Biogeographical Analysis of the Collembola (Arthropoda, Hexapoda) Unravels Recent Post-Glacial Colonization Patterns

We aimed to describe the main Arctic biogeographical patterns of the Collembola, and analyze historical factors and current climatic regimes determining Arctic collembolan species distribution. Furthermore, we aimed to identify possible dispersal routes, colonization sources and glacial refugia for Arctic collembola. We implemented a Gaussian Mixture Clustering method on species distribution ranges and applied a distance- based parametric bootstrap test on presence-absence collembolan species distribution data. Additionally, multivariate analysis was performed considering species distributions, biodiversity, cluster distribution and environmental factors (temperature and precipitation). No clear relation was found between current climatic regimes and species distribution in the Arctic. Gaussian Mixture Clustering found common elements within Siberian areas, Atlantic areas, the Canadian Arctic, a mid-Siberian cluster and specific Beringian elements, following the same pattern previously described, using a variety of molecular methods, for Arctic plants. Species distribution hence indicate the influence of recent glacial history, as LGM glacial refugia (mid-Siberia, and Beringia) and major dispersal routes to high Arctic island groups can be identified. Endemic species are found in the high Arctic, but no specific biogeographical pattern can be clearly identified as a sign of high Arctic glacial refugia. Ocean currents patterns are suggested as being an important factor shaping the distribution of Arctic Collembola, which is consistent with Antarctic studies in collembolan biogeography. The clear relations between cluster distribution and geographical areas considering their recent glacial history, lack of relationship of species distribution with current climatic regimes, and consistency with previously described Arctic patterns in a series of organisms inferred using a variety of methods, suggest that historical phenomena shaping contemporary collembolan distribution can be inferred through biogeographical analysis.

Post-glacial partitioning of mitochondrial genetic variation in the field vole

Genetic markers are often used to examine population history. There is considerable debate about the behaviour of molecular clock rates around the population-species transition. Nevertheless, appropriate calibration is critical to any inference regarding the absolute timing and scale of demographic changes. Here, we use a mitochondrial cytochrome b gene genealogy, based entirely on modern sequences and calibrated from recent geophysical events, to date the post-glacial expansion of the Eurasian field vole (Microtus agrestis), a widespread temperate mammal species. The phylogeographic structure reflects the subsequent expansion of populations that went through bottlenecks at the time of the Younger Dryas (ca 12,000 years BP) rather than the Last Glacial Maximum (LGM, ca 24,000 years BP), which is usually seen as the time when present-day patterns were determined. The nucleotide substitution rate that was estimated here, ca 4 × 10(-7) substitutions/site/year, remains extremely high throughout the relevant time frame. Calibration with similarly high population-based substitution rates, rather than long-term rates derived from species divergence times, will show that post-LGM climatic events generated current phylogeographic structure in many other organisms from temperate latitudes.

Microsatellite DNA analyses of a highly disjunct New Zealand tree reveal strong differentiation and imply a formerly more continuous distribution

Although New Zealand is a biodiversity hotspot, there has been little genetic investigation of why so many of its threatened and uncommon plants have naturally disjunct distributions. We investigated the small tree Pseudopanax ferox (Araliaceae), which has a widespread but highly disjunct lowland distribution within New Zealand. Genotyping of nuclear microsatellites and a chloroplast locus revealed pronounced genetic differentiation and four principal genetic clusters. Our results indicate that the disjunct distribution is a product of vicariance rather than long-distance dispersal. This highlights the need to preserve multiple populations when disjunct distributions are the result of vicariance, rather than focusing conservation efforts on a core area, in order to retain as much as possible of a species' evolutionary legacy and potential. Additionally, based on our genetic findings and the ecology of P. ferox, we hypothesize that it was more continuously distributed during the drier (but not maximally colder) interstadials of glacial periods and/or on the fertile soils available immediately postglacial. We further hypothesize that P. ferox belongs to a suite of species of drought-prone and/or fertile habitats whose distributions are actually restricted during warmer and wetter interglacial periods, despite being principally of the lowlands. Our genetic data for P. ferox are also the first consistent with the survival during the Last Glacial Maxima of a lowland tree at high latitudes in the south-eastern South Island.

Comparative phylogeography of two related plant species with overlapping ranges in Europe, and the potential effects of climate change on their intraspecific genetic diversity

BACKGROUND

The aim of the present study was to use a combined phylogeographic and species distribution modelling approach to compare the glacial histories of two plant species with overlapping distributions, Orthilia secunda (one-sided wintergreen) and Monotropa hypopitys (yellow bird's nest). Phylogeographic analysis was carried out to determine the distribution of genetic variation across the range of each species and to test whether both correspond to the "classic" model of high diversity in the south, with decreasing diversity at higher latitudes, or whether the cold-adapted O. secunda might retain more genetic variation in northern populations. In addition, projected species distributions based on a future climate scenario were modelled to assess how changes in the species ranges might impact on total intraspecific diversity in both cases.

RESULTS

Palaeodistribution modelling and phylogeographic analysis using multiple genetic markers (chloroplast trnS-trnG region, nuclear ITS and microsatellites for O. secunda; chloroplast rps2, nuclear ITS and microsatellites for M. hypopitys) indicated that both species persisted throughout the Last Glacial Maximum in southern refugia. For both species, the majority of the genetic diversity was concentrated in these southerly populations, whereas those in recolonized areas generally exhibited lower levels of diversity, particularly in M. hypopitys. Species distribution modelling based on projected future climate indicated substantial changes in the ranges of both species, with a loss of southern and central populations, and a potential northward expansion for the temperate M. hypopitys.

CONCLUSIONS

Both Orthilia secunda and Monotropa hypopitys appear to have persisted through the LGM in Europe in southern refugia. The boreal O. secunda, however, has retained a larger proportion of its genetic diversity in more northerly populations outside these refugial areas than the temperate M. hypopitys. Given that future species distribution modelling suggests northern range shifts and loss of suitable habitat in the southern parts of the species' current distributions, extinction of genetically diverse rear edge populations could have a significant effect in the rangewide intraspecific diversity of both species, but particularly in M. hypopitys.

Glacial refugia in pathogens: European genetic structure of anther smut pathogens on Silene latifolia and Silene dioica

Climate warming is predicted to increase the frequency of invasions by pathogens and to cause the large-scale redistribution of native host species, with dramatic consequences on the health of domesticated and wild populations of plants and animals. The study of historic range shifts in response to climate change, such as during interglacial cycles, can help in the prediction of the routes and dynamics of infectious diseases during the impending ecosystem changes. Here we studied the population structure in Europe of two Microbotryum species causing anther smut disease on the plants Silene latifolia and Silene dioica. Clustering analyses revealed the existence of genetically distinct groups for the pathogen on S. latifolia, providing a clear-cut example of European phylogeography reflecting recolonization from southern refugia after glaciation. The pathogen genetic structure was congruent with the genetic structure of its host species S. latifolia, suggesting dependence of the migration pathway of the anther smut fungus on its host. The fungus, however, appeared to have persisted in more numerous and smaller refugia than its host and to have experienced fewer events of large-scale dispersal. The anther smut pathogen on S. dioica also showed a strong phylogeographic structure that might be related to more northern glacial refugia. Differences in host ecology probably played a role in these differences in the pathogen population structure. Very high selfing rates were inferred in both fungal species, explaining the low levels of admixture between the genetic clusters. The systems studied here indicate that migration patterns caused by climate change can be expected to include pathogen invasions that follow the redistribution of their host species at continental scales, but also that the recolonization by pathogens is not simply a mirror of their hosts, even for obligate biotrophs, and that the ecology of hosts and pathogen mating systems likely affects recolonization patterns.