Beyond skepticism: uncovering cryptic refugia using multiple lines of evidence

Lafontaine, Guillaume de; Guerra, Carlos A. Amasifuén; Ducousso, Alexis; Sánchez-Goñi, María-Fernanda; Petit, Rémy J.

doi:10.1111/nph.13089

Cited by 25 publications

(21 citation statements)

References 35 publications

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“…; de Lafontaine et al. ). In contrast, the variations in Quaternary phylogeographic histories of plant species in topographically complex regions, such as the Qinghai–Tibet Plateau (QTP), are much more pronounced (e.g., Zhang et al.…”

Section: Introductionmentioning

confidence: 98%

The Quaternary evolutionary history, potential distribution dynamics, and conservation implications for a Qinghai–Tibet Plateau endemic herbaceous perennial, Anisodus tanguticus (Solanaceae)

Wan

Feng

Jiang

et al. 2016

Ecology and Evolution

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Various hypotheses have been proposed about the Quaternary evolutionary history of plant species on the Qinghai–Tibet Plateau (QTP), yet only a handful of studies have considered both population genetics and ecological niche context. In this study, we proposed and compared climate refugia hypotheses based on the phylogeographic pattern of Anisodus tanguticus (three plastid DNA fragments and nuclear internal transcribed spacer regions from 32 populations) and present and past species distribution models (SDMs). We detected six plastid haplotypes in two well‐differentiated lineages. Although all haplotypes could be found in its western (sampling) area, only haplotypes from one lineage occurred in its eastern area. Meanwhile, most genetic variations existed between populations (FST = 0.822). The SDMs during the last glacial maximum and last interglacial periods showed range fragmentation in the western area and significant range contraction in the eastern area, respectively, in comparison with current potential distribution. This species may have undergone intraspecific divergence during the early Quaternary, which may have been caused by survival in different refugia during the earliest known glacial in the QTP, rather than geological isolation due to orogenesis events. Subsequently, climate oscillations during the Quaternary resulted in a dynamic distribution range for this species as well as the distribution pattern of its plastid haplotypes and nuclear genotypes. The interglacial periods may have had a greater effect on A. tanguticus than the glacial periods. Most importantly, neither genetic data nor SDM alone can fully reveal the climate refugia history of this species. We also discuss the conservation implications for this important Tibetan folk medicine plant in light of these findings and SDMs under future climate models. Together, our results underline the necessity to combine phylogeographic and SDM approaches in future investigations of the Quaternary evolutionary history of species in topographically complex areas, such as the QTP.

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Section: Introductionmentioning

confidence: 98%

The Quaternary evolutionary history, potential distribution dynamics, and conservation implications for a Qinghai–Tibet Plateau endemic herbaceous perennial, Anisodus tanguticus (Solanaceae)

Wan

Feng

Jiang

et al. 2016

Ecology and Evolution

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“…; Huntley ; de Lafontaine et al . ,b). As we shall see, the current genetic structure at nuclear loci lends support to the general picture drawn by Tollefsrud et al .…”

Section: Introductionmentioning

confidence: 99%

The extent and meaning of hybridization and introgression between Siberian spruce (Picea obovata) and Norway spruce (Picea abies): cryptic refugia as stepping stones to the west?

et al. 2016

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Boreal species were repeatedly exposed to ice ages and went through cycles of contraction and expansion while sister species alternated periods of contact and isolation. The resulting genetic structure is consequently complex, and demographic inferences are intrinsically challenging. The range of Norway spruce (Picea abies) and Siberian spruce (Picea obovata) covers most of northern Eurasia; yet their geographical limits and histories remain poorly understood. To delineate the hybrid zone between the two species and reconstruct their joint demographic history, we analysed variation at nuclear SSR and mitochondrial DNA in 102 and 88 populations, respectively. The dynamics of the hybrid zone was analysed with approximate Bayesian computation (ABC) followed by posterior predictive structure plot reconstruction and the presence of barriers across the range tested with estimated effective migration surfaces. To estimate the divergence time between the two species, nuclear sequences from two well-separated populations of each species were analysed with ABC. Two main barriers divide the range of the two species: one corresponds to the hybrid zone between them, and the other separates the southern and northern domains of Norway spruce. The hybrid zone is centred on the Urals, but the genetic impact of Siberian spruce extends further west. The joint distribution of mitochondrial and nuclear variation indicates an introgression of mitochondrial DNA from Norway spruce into Siberian spruce. Overall, our data reveal a demographic history where the two species interacted frequently and where migrants originating from the Urals and the West Siberian Plain recolonized northern Russia and Scandinavia using scattered refugial populations of Norway spruce as stepping stones towards the west.

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“…Although a majority of temperate tree species survived the Late Pleniglacial (LPG), 24–15 kyr bp (Tzedakis et al ., ), presumably in southerly located refugia (i.e. the Iberian, Italian and Balkan peninsulas) according to the ‘southern refugia paradigm’ (Hewitt, ; but see Magri et al ., ; de Lafontaine et al ., , ,b), boreal tree species were probably distributed more widely (Tzedakis et al ., ). This is supported by the presence of genetically very rich populations found in the area north of the Alps (e.g.…”

Section: Introductionmentioning

confidence: 99%

Recent similarity in distribution ranges does not mean a similar postglacial history: a phylogeographical study of the boreal tree species Alnus incana based on microsatellite and chloroplast DNA variation

et al. 2016

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SummaryWe reconstructed the historical pattern of postglacial biogeographic range expansion of the boreal tree species Alnus incana in Europe.To assess population genetic structure and diversity, we performed a combined analysis of nuclear microsatellite loci and chloroplast DNA sequences (65 populations, 1004 individuals).Analysis of haplotype and microsatellite diversity revealed that southeastern refugial populations situated in the Carpathians and the Balkan Peninsula did not spread north and cannot be considered as important source populations for postglacial recolonization of Europe; populations in Eastern Europe did not establish Fennoscandian populations; populations in Fennoscandia and Eastern Europe have no unique genetic cluster, but represent a mix with a predominant cluster typical for Central Europe; and that colonization of Fennoscandia and Eastern Europe took place from Central Europe.Our findings highlight the importance of an effective refugium in Central Europe located outside classical southern refugia confirming the existence of northern refugia for boreal trees in Europe. The postglacial range expansion of A. incana did not follow the model established for Picea abies. Fennoscandian populations are not derived from Eastern European ones, but from Central European ones.

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Beyond skepticism: uncovering cryptic refugia using multiple lines of evidence

Cited by 25 publications

References 35 publications

The Quaternary evolutionary history, potential distribution dynamics, and conservation implications for a Qinghai–Tibet Plateau endemic herbaceous perennial, Anisodus tanguticus (Solanaceae)

The Quaternary evolutionary history, potential distribution dynamics, and conservation implications for a Qinghai–Tibet Plateau endemic herbaceous perennial, Anisodus tanguticus (Solanaceae)

The extent and meaning of hybridization and introgression between Siberian spruce (Picea obovata) and Norway spruce (Picea abies): cryptic refugia as stepping stones to the west?

Recent similarity in distribution ranges does not mean a similar postglacial history: a phylogeographical study of the boreal tree species Alnus incana based on microsatellite and chloroplast DNA variation

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