A range-wide synthesis and timeline for phylogeographic events in the red fox (Vulpes vulpes)
Author(s): Kutschera, VE, Hailer, F
Many boreo-temperate mammals have a Pleistocene fossil record throughout Eurasia and North America, but only few have a contemporary distribution that spans this large area. Examples of Holarctic-distributed carnivores are the brown bear, grey wolf and red fox, all three ecological generalists with large dispersal capacity and a high adaptive flexibility. While the two former have been examined extensively across their ranges, no phylogeographic study of the red fox has been conducted across its entire Holarctic range. Moreover, no study included samples from central Asia, leaving a large sampling gap in the middle of the Eurasian landmass. We obtained the first mitochondrial DNA sequence data of red foxes from Siberia, and new sequences from several European populations. In a range-wide synthesis of more than 500 previously published and publicly available red fox mitochondrial control region sequences and 52 newly obtained sequences, we describe the pattern and timing of major phylogeographic events in red foxes, using a Bayesian coalescence approach with multiple fossil tip and root calibration points. All newly sequenced individuals belonged to the previously described Holarctic lineage. Our analyses confirmed the presence of three Nearctic- and two Japan-restricted lineages that were formed since the Mid/Late Pleistocene. The phylogeographic history of red foxes is highly similar to that previously described for grey wolves and brown bears, indicating that climatic fluctuations and habitat changes since the Pleistocene had similar effects on these highly mobile generalist species. All three species originally diversified in Eurasia and later colonized North America and Japan several times independently. North American lineages persisted through the last glacial maximum south of the ice sheets, meeting more recent colonizers from Beringia during postglacial expansion into the northern Nearctic.
Department of Biological Science
Anchored Phylogenomics: Accelerating the Resolution of Life
Author(s): Lemmon, EM
The field of phylogenomics is undergoing a revolution, enabled by new methods of data collection that leverage both genomic resources and recent advances in DNA sequencing. We developed a cost-efficient and rapid approach to obtaining data from 100s to 1000s of loci and individuals for deep and shallow phylogenetic studies. Specifically, we designed probes for target hybrid enrichment of 100s of loci in conserved anchor regions of genomes (flanked by less conserved regions). We enriched genomic DNA libraries for these anchor regions, and sequenced these targets using high-throughput sequencing. The resulting data sets contain 100s of loci with low levels of missing data and high levels of phylogenetic information across taxonomic scales and produce phylogenies with high levels of resolution. This approach is expediting resolution of deep-scale portions of the Tree of Life and greatly accelerating resolution of the large number of shallow clades that remain unresolved. The combination of low cost (∼1% of the cost of traditional Sanger sequencing and ∼3.5% of the cost of high-throughput amplicon sequencing for projects on the scale of 500 loci × 100 individuals) and rapid data collection (∼2 weeks of laboratory time) make this approach tractable even for researchers working on systems with limited genomic resources. Here, I present new work from vertebrates and unpublished data from various non-vertebrate (e.g., Coleoptera, Hymenoptera, etc.) and plant (e.g., Angiosperm) clades; I also discuss future directions and new applications.
Assessing the confounding effect of population structure on Bayesian skyline plot inferences of demographic history
Author(s): Heller, R, Chikhi, L, Siegismund, HR
It is well known that population structure can confound coalescent-based inferences of past population size changes when it is not properly accounted for. Although the vast majority of species are genetically structured to some extent, few studies have quantified how different types and levels of structure might confound demographic inference. Among the most widely applied demographic inference methods is the Bayesian skyline plot (BSP and the derived EBSP), which assume a panmictic model without structure. We simulated DNA sequence data under a variety of scenarios involving structured populations with variable levels of gene flow and analysed them using EBSPs as implemented in the software package BEAST. Results revealed that BSPs can show false signals of population decline under several biologically plausible combinations of population structure and sampling strategy, suggesting that the interpretation of several previous studies may need to be re-evaluated. We found that sampling strategies present a trade-off between minimizing the risk of false positives and maximizing the power to detect recent demographic events. Therefore, a balanced sampling strategy whereby samples are distributed over several populations provides the best scheme for inferring demographic change over the time scale that is typically of interest. Case studies demonstrate that although the structure effect should always be accounted for, some systems will be more susceptible than others. Our study provides a much-needed quantification of the structure effect in BSP analyses and some practical guidelines to keep in mind before attempting such analyses.
Environmental Futures Centre
Avian malaria diversity in southern Melanesia: exploring potential influences on distribution patterns and divergence of host bird species
Author(s): Clegg, S, Olsson-Pons, S, Clark, N, Ishtiaq, F
Host-pathogen interactions have the potential to influence broad scale ecological and evolutionary processes in host populations, influencing levels of endemism, divergence patterns and distributions. The development of localized co-adapted host-pathogen relationships could drive divergent selection and limit gene flow among populations of the same species or limit range expansions of closely related species. To examine the potential for pathogens to direct these types of processes in natural host populations, we explored the phylogenetic diversity and prevalence of avian malaria parasites, and the distribution of lineages across islands and host species, in southern Melanesian bird communities. We uncovered high avian malaria diversity, including many rare lineages, pointing to high estimates of undiscovered lineage richness in the region. While significant phylogeographic structuring of parasite lineages was detected, most genetic variation was distributed within rather than between island locations. Only a small number of lineages could be considered generalist with respect to host species infection. Parasite lineage-host associations were evident at the host family and host species level, and in a few cases, at the local host population level. Prevalence varied significantly among islands, but not among host species, and for three widely sampled host species, there was a significant interaction term demonstrating variation in prevalence in different populations of the same species. The heterogeneity demonstrated in both the complement and the prevalence of parasite lineages infecting local avian communities likely exposes species to a mosaic of disease-related selection pressures across their naturally fragmented distributions in southern Melanesia. Therefore interactions between avian malaria parasites and their avian hosts are an important factor to consider when examining avian divergence and distribution patterns in this region.
Departmento de Biología
Co-divergence between bacteria and host: Consequences of Wolbachia infection in the Chorthippus parallelus hybrid zone
Author(s): Martínez-Rodríguez, P, Arroyo-Yebras, F, Bella, JL
Divergence between two subspecies of the grasshopper Chorthippus parallelus has been extensively studied for evolutionary purposes. They form a hybrid zone in the Pyrenees between the Iberian endemic subspecies C. p. erythropus and the continental European subspecies C. p. parallelus (1). Wolbachia infection in pure and hybrid individuals of these subspecies has been characterized by PCR analysis of their 16S rRNA sequences and a Multi-Locus Strain Typing System (MLST) (2). Phylogenetic and phylogeographic studies based on previous host phylogeny, as well as this MLST approach, show that Wolbachia co-diverges with its host. In addition, extrapolation of the divergence time between bacterial strains allows us to propose than Wolbachia infected C. parallelus during host speciation. This fact, joint to the cytoplasmic incompatibility and other effects induced by this bacterium in natural populations of C. parallelus (3, 4) support that co-divergence between bacteria and host contributes to explain the current situation of the hybrid zone.
(1) Shuker DM, et al. 2005. “The genetic basis of speciation in a grasshopper hybrid zone”. En “Insect Evolutionary Ecology”. CABI Publishing, Oxford University Press, pp 427-454. ISBN 0851998127. (2) Baldo L, et al. 2006. Multilocus Sequence Typing System for the Endosymbiont Wolbachia pipientis. Appl Environ Microbiol 72:7098-7110. (3) Bella, J.L, Martínez-Rodríguez, P., Arroyo-Yebras, F., Bernal, A., Sarasa, J., Fernández-Calvín, B, Mason, P.L. & Zabal-Aguirre, M. 2010. “Wolbachia infection in the Chorthippus parallelus hybrid zone: evidence for its role as a reproductive barrier”. Journal of Orthoptera Research, 19 (2): 205-212. (4) Sarasa, J., Bernal, A., Fernández-Calvín, B. & Bella, J.L. 2013. Wolbachia induced cytogenetical effects, as evidenced in Chorthippus parallelus (Orthoptera). Cytogenetic and Genome Research 139: 36–43.
Comparative phylogeography of African rain forest trees: a review of genetic signatures of vegetation history in the Guineo-Congolian region
Author(s): Hardy, OJ
The biogeographic history of the African rain forests has been contentious. Phylogeography, the study of the geographic distribution of genetic lineages within species, can highlight the signatures of historical events affecting the demography and distribution of species (population fragmentation or size changes, range expansion/contraction) and, thereby, the ecosystems they belong to. The accumulation of recent data for African rain forest plants now enables a first biogeographic synthesis. In this review, we explain which phylogeographic patterns are expected under different scenarios of past demographic changes; and we give an overview of the patterns detected in African rain forest trees to discuss whether they support alternative hypotheses regarding the history of the African rain forest cover. Phylogeographic patterns indicate that most of the widespread species showing nowadays a near continuous spatial distribution have been fragmented in the past. The major genetic discontinuities in the region support the role of refugia during climatic oscillations, and at a large scale they often match the main phytogeographic subdivision of the Guineo-Congolian region. However, patterns vary substantially among species and they provide only partial support for current hypotheses on the location of Pleistocene forest refuges. Among the patterns shared by many species, we highlight a recurrent genetic discontinuity between the north and the south of the Lower Guinean region which matches the climatic hinge on each side of which dry and wet seasons are inverted. Whether this discontinuity results from past forest fragmentation or current climate conditions is discussed.
Department of Botany
Comparative phylogeography of three tree species from the Albany Subtropical Thicket of South Africa: testing cornerstone hypotheses of a large-scale conservation network
Author(s): Potts, AJ, Hedderson, TA, Cowling, RM
An ambitious large-scale network of conservation areas and corridors has been designed with the aim of preserving the evolutionary patterns and processes of the Albany Subtropical Thicket biome of South Africa. Two main hypotheses, largely based on expert opinion, formed the foundation for this conservation plan: 1) drainage basins are discrete biogeographical, and thus evolutionarily-distinct, units, and 2) long-distance movement of the primary agents of disturbance in this landscape, African elephants (Loxodonta africana), is critical for ecosystem functioning. Here we test these hypotheses using chloroplast phylogeography of three tree species with similar ecologies but different seed dispersal syndromes, specifically Nymania capensis (Meliaceae; inflated wind-dispersed seeds), Pappea capensis (Sapindaceae; small bird-dispersed seeds) and Schotia afra (Fabaceae, large seed-pods dispersed by elephants and other large mammals). Each drainage basin was found to have isolated populations of the wind- and bird-dispersed species, whereas the elephant-dispersed species has a single regional meta-population that extends across all the drainage basins. These results suggest that the deeply-incised drainage basins along the coastal lowlands of South Africa are unique phylogeographic, as well as biogeographic, units for species that that lack long-distance dispersal mechanisms over such a topographically-complex landscape. At present, elephants and many other large herbivores are restricted to an extremely reduced and fragmented proportion of their historical distribution along the coastal lowlands. The phylogeographic patterns of S. afra highlight the importance of re-establishing the free movement of megaherbivores across the regional landscape for this and other elephant-dispersed plants. These phylogeographic patterns offer pivotal support for the proposed network of conservation corridors for this biome.
Ecologie des Forêts Prairies et Milieux Aquatiques
Dispersal, gene flow and ecological speciation in lampreys
Author(s): Rougemont, Q, Gaigher, A, Launey, S, Lasne, E, Besnard, A, Evanno, G
In species with complex life histories estimates of dispersal rates can be obtained from genetic data. This approach allows comparing levels of intraspecific gene flow among species with different dispersal abilities. Lampreys evolved as either anadromous species (i.e. reproducing in freshwater but growing mainly at sea) with a parasitic lifestyle at sea or as non-parasitic freshwater resident species. Anadromous species home to their natal river or disperse to other rivers and should thus display higher level of gene flow among populations than resident species. The three European lamprey species allow testing this prediction: Lampetra planeri (LP) is resident in freshwater while L. fluviatilis (LF) and Petromyzon marinus (PM) are anadromous. LF and LP are morphologically and phylogenetically very similar and they may represent two ecotypes of a single species. We investigated the genetic structure among LP, LF and PM populations in France to i) test whether levels of gene flow are higher in anadromous than in resident species and ii) measure the level of gene flow among sympatric LF and LP populations. We used microsatellite loci to genotype 665 LF and LP and 380 PM individuals. Our results show a gradient of increasing genetic differentiation among lamprey species (PM < LF < LP) suggesting that populations of anadromous species are connected by higher levels of gene flow than LP populations. Interestingly, we detected some gene flow among sympatric LF and LP populations supporting the hypothesis that these species are actually two ecotypes of a single species possibly at an early stage of ecological speciation. In addition, estimates of genetic diversity were significantly higher in LF than LP populations. These results have important implications for conservation management through the definition of evolutionary significant units and species boundaries. They also suggest that the connectivity between putative LP and LF ecotypes should be maintained.
Institute of Environmental Sciences
Divergence and gene flow in Lissotriton newts
Author(s): Babik, W, Zieliński, P, Stuglik, MT
Historical patterns and consequences of genetic exchange between hybridizing species are poorly understood, but new genomic and analytical tools promise a rapid progress. We will present the results of research on historical demography and genome-wide patterns of gene flow between hybridizing newts Lissotriton montandoni (Lm) and L. vulgaris (Lv). These newts are characterized by a long history of genetic exchange, as evidenced by the mitochondrial DNA (mtDNA) data. Multiple, spatially and temporally distinct introgression events from Lv resulted in complete mtDNA replacement in Lm. We used various classes of molecular nuclear markers to obtain information about the extent and historical patterns of gene flow between the two species. Fifteen microsatellite loci and 139 coding SNPs surveyed in multiple populations demonstrated a very limited recent admixture in the nuclear genome. Genome-wide patterns of long-term gene flow were assessed by analyzing of over 300 000 SNPs derived from high-throughput transcriptome sequencing. The inferences based on the joint two-population allele frequency spectrum revealed an extensive, asymmetric gene flow from Lv to Lm and models allowing for demographic changes and temporal variation in the strength of gene flow provided best fit to the data. The species distribution modeling based on contemporary and historical climatic data suggests that temporal variation in gene flow between Lm and Lv may be linked to range changes the newts experienced during the Pleistocene climatic oscillations. Sequences of over 50 nuclear markers collected throughout the species ranges and analyzed within the coalescent framework provided evidence for genomic heterogeneity in gene flow. Our study demonstrates the complexity of long-term genetic exchange between hybridizing species and the power of new sequencing technologies for a comprehensive characterization of interspecific gene flow in non-model organisms possessing huge genomes.
Department of Animal Biology
From Africa and back again: biogeography and differentiation of a specialist west-Mediterranean butterfly in a fragmented glacial refuge
Author(s): Marabuto, E, Rebelo, M, Paulo, OS
The Mediterranean area is well known for retaining and generating biodiversity during climate and habitat shifts taking place since the end of the Miocene. This important biodiversity hotspot is both the source and the result of a complex process of differentiation and interaction between evolving lineages and their changing environment. However, regarding stationary Mediterranean specialists, which are expected to benefit and expand northwards with climate amelioration, little is still known. Using the butterfly Euchloe tagis, an Atlanto-Mediterranean ecological specialist with a fragmented and restricted distribution, this study attempts at answering pertinent biogeographic aspects on the species and its interaction with the changing ecosystem. We sequenced a 599bp barcode region fragment of the COI gene from all major populations to better understand current its genetic patterns and evolutionary history. Main results suggest an origin in North Africa, from where the sister species Euchloe pechi is endemic. While one of the Moroccan populations diverged earlier from the remaining stock, all remaining are more closely related despite the existence of differentiated major mitochondrial lineages. It seems that Iberia has played a pivotal role in the generation of diversity in this species: two consistent genetic clusters are partly sympatric whereas French and Italian populations are considerably different. The second Moroccan population from the Rif Mountains shows little segregation from French samples and this issue is discussed on a phylogeographic framework supported by molecular-clock analysis. This pattern suggests this species experienced polycentric refugia during climate cycles, leading to such genetic structure and a putative re-colonization of Africa. Moreover, the neutral genetic pattern reported in this study challenges current taxonomy based on morphological differentiation and suggests a more complex evolution of this species.