Phylogeographic analysis of the red seaweed Palmaria palmata reveals a Pleistocene marine glacial refugium in the English Channel

Phylogeography has provided a new approach to the analysis of the postglacial history of a wide range of taxa but, to date, little is known about the effect of glacial periods on the marine biota of Europe. We have utilized a combination of nuclear, plastid and mitochondrial genetic markers to study the biogeographic history of the red seaweed Palmaria palmata in the North Atlantic. Analysis of the nuclear rDNA operon (ITS1-5.8S-ITS2), the plastid 16S-trnI-trnA-23S-5S, rbcL-rbcS and rpl12-rps31-rpl9 regions and the mitochondrial cox2-3 spacer has revealed the existence of a previously unidentified marine refugium in the English Channel, along with possible secondary refugia off the southwest coast of Ireland and in northeast North America and/or Iceland. Coalescent and mismatch analyses date the expansion of European populations from approximately 128,000 BP and suggest a continued period of exponential growth since then. Consequently, we postulate that the penultimate (Saale) glacial maximum was the main event in shaping the biogeographic history of European P. palmata populations which persisted throughout the last (Weichselian) glacial maximum (c. 20,000 BP) in the Hurd Deep, an enigmatic trench in the English Channel.     

Mitochondrial DNA sequence analysis reveals multiple Pleistocene glacial refugia for the Yellow‐spotted mountain newt,Neurergus derjugini (Caudata: Salamandridae) in the mid‐Zagros range in Iran and Iraq

Phylogeography is often used to investigate the effects of glacial cycles on current genetic structure of various plant and animal species. This approach can also identify the number and location of glacial refugia as well as the recolonization routes from those refugia to the current locations. To identify the location of glacial refugia of the Yellow‐spotted mountain newt, Neurergus derjugini, we employed phylogeography patterns and genetic variability of this species by analyzing partial ND4 sequences (867 bp) of 67 specimens from 15 sampling localities from the whole species range in Iran and Iraq. Phylogenetic trees concordant with haplotype networks showed a clear genetic structure among populations as three groups corresponding to the populations in the north, center, and south. Evolutionary ages of clades north and south ranging from 0.15 to 0.17 Myr, while the oldest clade is the central clade, corresponding to 0.32 Myr. Bayesian skyline plots of population size change through time show a relatively slight increase until about 25 kyr (around the last glacial maximum) and a decline of population size about 2.5 kyr. The presence of geographically structured clades in north, center, and south sections of the species range signifies the disjunct populations that have emerged in three different refugium. This study illustrates the importance of the effect of previous glacial cycles in shaping the genetic structure of mountain species in the Zagros range. These areas are important in terms of long‐term species persistence and therefore valuable areas for conservation of biodiversity.     

Migration patterns of Gentiana crassicaulis,an alpine gentian endemic to the Himalaya–Hengduan Mountains

The Himalaya–Hengduan Mountain region is one of the hotspots of biodiversity research. The uplift of the Qinghai–Tibetan Plateau (QTP) and the Quaternary glaciation caused great environmental changes in this region, and the responses of many species in the QTP to the Quaternary climate are still largely unknown. The genetic structure and phylogeographical history of Gentiana crassicaulis Duthie ex Burk, an endemic Chinese alpine species in this area, were investigated based on four chloroplast fragments and internal transcribed spacer region of the nuclear ribosomal DNA (nrITS) sequences of 11 populations. The populations with highly diverse chloroplast haplotypes were mainly found at the edge of the QTP. There were two main haplotypes of nrITS clones, one shared by the Yunnan and Guizhou populations, and the other by the remaining populations. The population with the highest diversity was the Gansu population, located at the edge of the plateau. Based on molecular dating, the diversification of G. crassicaulis at the edge of the plateau occurred before the Last Glacial Maximum (LGM), and the species may have completed its expansion from the edge to the platform. Ecological niche models were conducted to predict the distributional ranges of G. crassicaulis at present, during the LGM, and during the last interglacial (LIG) period. The results demonstrated that G. crassicaulis survived on the QTP platform and at the edge during the LGM but afterward retreated from the platform to the southern edge, followed by expansion to the platform.     

Refugia within refugia: the case study of a canopy tree (Eurycorymbus cavaleriei) in subtropical China

Aim Eurycorymbus cavaleriei (Lévl.) Rehd. et Hand.‐Mazz. (Sapindaceae) is a Tertiary relict tree endemic to subtropical China. This area is a centre for speciation and evolution within the East Asia biome and one of its most important refugial locations. In this study we aim to elucidate the phylogeographical patterning in E. cavaleriei, in order to identify the locations of the species’ main refugia and the predominant patterns of migration that have led to the contemporary spatial genetic structure of chloroplast variation. Location Subtropical China. Methods We sampled 18 populations of E. cavaleriei throughout its geographical range. Chloroplast DNA (cpDNA) sequence data from two non‐coding regions ((trnS/trnG and pl20/5′‐rps12) were obtained from 170 individuals for phylogeographical analyses. Relationships among cpDNA haplotypes were determined using median‐joining networks. Genetic structure was examined by spatial analysis of molecular variance (SAMOVA). Population differentiation was estimated by G_ST and N_ST statistics. Results Ten distinct haplotypes were identified. The level of differentiation among populations was relatively high (G_ST = 0.817), and N_ST was significantly higher than G_ST (P < 0.05), indicating that strong phylogeographical structure is exhibited by this species. The SAMOVA revealed five diverging groups of related haplotypes, which coincide with major landscape features in this region. Main conclusions The high differentiation among populations of E. cavaleriei may be a combined effect of historical and contemporary processes, such as the low effective population size for the chloroplast genome of a dioecious species, long‐term range fragmentation and limited seed dispersal for the species. Clear‐cut geographical distributions of ancestral haplotypes of the species suggest multiple potential refugia across subtropical China. The identified refugial regions have long been recognized as centres of plant diversity and endemism for China and have also been suggested as glacial refugia for many other plant species. The combination of these factors means that these locations should be considered as the highest priority for inclusion in conservation policies and sustainable forest management strategies for subtropical China.     

Phylogeography of the pool frog Rana (Pelophylax) lessonae in the Italian peninsula and Sicily: multiple refugia,glacial expansions and nuclear–mitochondrial discordance

Aim To infer the evolutionary history of Rana (Pelophylax) lessonae Camerano within its inferred Quaternary refugial range, and to shed light on the processes that have contributed to shaping the patterns of diversity within the southern European peninsulas. Location The Italian peninsula south of the Alps and Sicily. Methods Sequence analysis of a mitochondrial cytochrome b gene fragment in 149 individuals sampled from 25 localities. Results Three mitochondrial DNA (mtDNA) phylogroups were identified, distributed in northern Italy, the whole Italian peninsula south of the northern Apennines, and Sicily. Syntopy between the northern and peninsular lineages was observed close to the northern Apennines. The northern lineage was the most differentiated, showing a net sequence divergence of 4.8 ± 0.8% with respect to the two others, whereas the net divergence between peninsular and Sicilian lineages was 2.6 ± 0.6%. Analysis of molecular variance (amova ) revealed that 93% of the overall variation occurred between these three groups. Historical demographic statistics support a recent expansion for both the northern and peninsular groups, but not for the Sicilian group. In both northern and peninsular Italy, such an expansion was likely to have occurred during the last glaciation. Main conclusions Our results suggest that a number of microevolutionary processes were involved in shaping the present genetic structure of R. lessonae in Italy. These encompass allopatric differentiations in three distinct Pleistocene refugia, recent population expansions and secondary contacts. Our results, together with some previous work, support (1) the existence of a suture zone in the northern Apennines, and (2) the possibility of population expansions during the last glacial phase, when a vast widening of the lowland floodplain habitats followed sea‐level fall, particularly in northern Italy. When compared with previous analyses of allozyme data, it appears that the peninsular mtDNA lineage has recently replaced the Sicilian one in southern Calabria, and we suggest that this event occurred due to selective introgression. The implications of such an occurrence for the study of factors underlying the patterns of diversity within this southern European biodiversity hotspot are discussed. Taxonomic implications of the results are also evaluated.     

Chloroplast DNA variation and phylogeography of Ligularia tongolensis (Asteraceae), a species endemic to the Hengduan Mountains region of China

In this research, we aimed to study the genetic variation and phylogeographic pattern of Ligularia tongolensis, a perennial herb endemic to the Hengduan Mountains region of China. We sequenced two chloroplast DNA (cpDNA) intergenic spacers (trnQ-5 rps16, trnL-rpl32) in 140 individuals from 14 populations of three groups (Jinshajiang vs. Yalongjiang vs. Wumeng) within this species range. High levels of haplotype diversity (Hd = 0.814) and total genetic diversity (Ht = 0.862) were detected at the species leve...     

A long‐standing Pleistocene refugium in southern Africa and a mosaic of refugia in East Africa: insights from mtDNA and the common eland antelope

Aim Previous genetic studies of African savanna ungulates have indicated Pleistocene refugial areas in East and southern Africa, and recent palynological, palaeovegetation and fossil studies have suggested the presence of a long‐standing refugium in the south and a mosaic of refugia in the east. Phylogeographic analysis of the common eland antelope, Taurotragus oryx (Bovidae), was used to assess these hypotheses and the existence of genetic signatures of Pleistocene climate change. Location The sub‐Saharan savanna biome of East and southern Africa. Methods Mitochondrial DNA control‐region fragments (414 bp) from 122 individuals of common eland were analysed to elucidate the phylogeography, genetic diversity, spatial population structuring, historical migration and demographic history of the species. The phylogeographic split among major genetic lineages was dated using Bayesian coalescent‐based methods and a calibrated fossil root of 1.6 Ma for the split between the common eland and the giant eland, Taurotragus derbianus. Results Two major phylogeographic lineages comprising East and southern African localities, respectively, were separated by a net nucleotide distance of 4.7%. A third intermediate lineage comprised only three haplotypes, from Zimbabwe in southern Africa. The estimated mutation rate of 0.097 Myr^?1 revealed a more recent common ancestor for the eastern lineage (0.21 Ma; 0.07–0.37) than for the southern lineage (0.35 Ma; 0.10–0.62). Compared with the latter, the eastern lineage showed pronounced geographic structuring, lower overall nucleotide diversity, higher population differentiation, and isolation‐by‐distance among populations. Main conclusions The data support the hypothesis of Pleistocene refugia occurring in East and southern Africa. In agreement with palynological, palaeovegetation and fossil studies, our data strongly support the presence of a longer‐standing population in the south and a mosaic of Pleistocene refugia in the east, verifying the efficacy of genetic tools in addressing such questions. The more recent origin of the common eland inhabiting East Africa could result from colonization following extinction from the region. Only two other dated African ungulate phylogenies have been published, applying different methods, and the similarity of dates obtained from the three distinct approaches indicates a significant event c. 200 ka, which left a strong genetic signature across a range of ungulate taxa.     

Multiple genetic divergences and population expansions of a Mediterranean sandfly,Phlebotomus ariasi,in Europe during the Pleistocene glacial cycles

Phlebotomus ariasi is one of the two sandflies transmitting the causative agent of zoonotic leishmaniasis, Leishmania infantum, in France and Iberia, and provides a rare case study of the postglacial re-colonization of France by a Mediterranean species. Four DNA sequences were analysed—mitochondrial cytochrome b (cyt b), nuclear elongation factor-1α (EF-1α) and two anonymous nuclear loci—for 14–15 French populations and single populations from northeast Spain, northwest Spain, Portugal and Morocco. The presence of cryptic sibling species was not revealed by phylogenetic analyses and testing for reproductive isolation between sympatric populations defined by the two most divergent cyt b haplogroups. No locus was shown to be under positive directional or balancing selection and, therefore, molecular variation was explained demographically. Each nuclear locus showed shallow isolation by distance from Portugal to the French Pyrenees, but for both cyt b and EF-1α there was then a step change to the upland Massif Central, where leading-edge populations showed low diversity at all loci. Multiple genetic divergences and population expansions were detected by analyses of cyt b and dated to the Pleistocene. Endemicity of one cyt b sub-lineage suggested the presence of a refuge north of the Pyrenees during the last glacial period. Monopolization of the Massif Central by genetically differentiated populations of P. ariasi might possibly hinder the northwards spread of leishmaniasis.     

r/K‐like trade‐off and voltinism discreteness: The implication to allochronic speciation in the fall webworm,Hyphantria cunea complex (Arctiidae)

North America has distinct types of Hyphantria moths (Arctiidae) characterized by red (RD)‐ and black (BL)‐headed larvae, of which the taxonomic status is unresolved. Genetic divergence of 26 populations, based on 710 bp of the mtCOI sequence, showed two phylogenetic lineages, which could not be connected in the haplotype network with 95% confidence. The two lineages are separated by 3.1% sequence divergence and should be considered for full species status. The estimated split occurred 1.2–1.6 million years ago. The range of the RD type covered most of the continent, whereas that of the BL type was limited to eastern deciduous forests. Several biological characteristics were differentiated in the zone of cohabitation where BL had more annual generations than RD. Spring emergence of BL precedes that of RD in the field by at least 1 month, because the diapause in BL was shallow, whereas it was deep in RD. Voltinism requires discreteness of numbers, which functions as a sink of hybrids between the two parental lines that have distinct but equally adaptive reproductive strategies; BL may be more r‐strategist‐like and RD more K‐strategist‐like, because fast‐developing BL has multivoltine life cycle, investing less silk proteins as the round‐the‐clock feeder, and slow‐developing RD univoltine one investing more silk as the nocturnal feeder. Also, intensity of diapause, deep in RD and weak in BL, was grossly different, which may enforce segregation of spring adults. Allochronic speciation avoiding coincidental occurrence of adult stages is therefore the most likely scenario. Because the adults never meet in nature, large morphological differentiation is not required.     

Genetic structure in the European endemic seabird,Phalacrocorax aristotelis,shaped by a complex interaction of historical and contemporary,physical and nonphysical drivers

Geographically separated populations tend to be less connected by gene flow, as a result of physical or nonphysical barriers preventing dispersal, and this can lead to genetic structure. In this context, highly mobile organisms such as seabirds are interesting because the small effect of physical barriers means nonphysical ones may be relatively more important. Here, we use microsatellite and mitochondrial data to explore the genetic structure and phylogeography of Atlantic and Mediterranean populations of a European endemic seabird, the European shag, Phalacrocorax aristotelis, and identify the primary drivers of their diversification. Analyses of mitochondrial markers revealed three phylogenetic lineages grouping the North Atlantic, Spanish/Corsican and eastern Mediterranean populations, apparently arising from fragmentation during the Pleistocene followed by range expansion. These traces of historical fragmentation were also evident in the genetic structure estimated by microsatellite markers, despite significant contemporary gene flow among adjacent populations. Stronger genetic structure, probably promoted by landscape, philopatry and local adaptation, was found among distant populations and those separated by physical and ecological barriers. This study highlights the enduring effect of Pleistocene climatic changes on shag populations, especially within the Mediterranean Basin, and suggests a role for cryptic northern refugia, as well as known southern refugia, on the genetic structure of European seabirds. Finally, it outlines how contemporary ecological barriers and behavioural traits may maintain population divergence, despite long‐distance dispersal triggered by extreme environmental conditions (e.g. population crashes).     

Land masses and oceanic currents drive population structure of Heritiera littoralis,a widespread mangrove in the Indo‐West Pacific

Phylogeographic forces driving evolution of sea‐dispersed plants are often influenced by regional and species characteristics, although not yet deciphered at a large spatial scale for many taxa like the mangrove species Heritiera littoralis. This study aimed to assess geographic distribution of genetic variation of this widespread mangrove in the Indo‐West Pacific region and identify the phylogeographic factors influencing its present‐day distribution. Analysis of five chloroplast DNA fragments’ sequences from 37 populations revealed low genetic diversity at the population level and strong genetic structure of H. littoralis in this region. The estimated divergence times between the major genetic lineages indicated that glacial level changes during the Pleistocene epoch induced strong genetic differentiation across the Indian and Pacific Oceans. In comparison to the strong genetic break imposed by the Sunda Shelf toward splitting the lineages of the Indian and Pacific Oceans, the genetic differentiation between Indo‐Malesia and Australasia was not so prominent. Long‐distance dispersal ability of H. littoralis propagules helped the species to attain transoceanic distribution not only across South East Asia and Australia, but also across the Indian Ocean to East Africa. However, oceanic circulation pattern in the South China Sea was found to act as a barrier creating further intraoceanic genetic differentiation. Overall, phylogeographic analysis in this study revealed that glacial vicariance had profound influence on population differentiation in H. littoralis and caused low genetic diversity except for the refugia populations near the equator which might have persisted through glacial maxima. With increasing loss of suitable habitats due to anthropogenic activities, these findings therefore emphasize the urgent need for conservation actions for all populations throughout the distribution range of H. littoralis.     

Linking ecology,morphology, and metabolism: Niche differentiation in sympatric populations of closely related species of the genus Littorina (Neritrema)

Divergence of ecological niches in phylogenetically closely related species indicates the importance of ecology in speciation, especially for sympatric species are considered. Such ecological diversification provides an advantage of alleviating interspecies competition and promotes more efficient exploitation of environmental resources, thus being a basis for ecological speciation. We analyzed a group of closely related species from the subgenus Neritrema (genus Littorina, Caenogastropoda) from the gravel‐bouldery shores. In two distant sites at the Barents and Norwegian Sea, we examined the patterns of snail distribution during low tide (quantitative sampling stratified by intertidal level, presence of macrophytes, macrophyte species, and position on them), shell shape and its variability (geometric morphometrics), and metabolic characteristics (metabolomic profiling). The studied species diversified microbiotopes, which imply an important role of ecological specification in the recent evolution of this group. The only exception to this trend was the species pair L. arcana / L. saxatilis, which is specifically discussed. The ecological divergence was accompanied by differences in shell shape and metabolomic characteristics. Significant differences were found between L. obtusata versus L. fabalis and L. saxatilis / L. arcana versus L. compressa both in shell morphology and in metabolomes. L. saxatilis demonstrated a clear variability depending on intertidal level which corresponds to a shift in conditions within the occupied microhabitat. Interestingly, the differences between L. arcana (inhabiting the upper intertidal level) and L. compressa (inhabiting the lower one) were analogous to those between the upper and lower fractions of L. saxatilis. No significant level‐dependent changes were found between the upper and lower fractions of L. obtusata, most probably due to habitat amelioration by fucoid macroalgae. All these results are discussed in the contexts of the role of ecology in speciation, ecological niche dynamics and conservatism, and evolutionary history of the Neritrema species.     

Idiosyncratic responses to climate‐driven forest fragmentation and marine incursions in reed frogs from Central Africa and the Gulf of Guinea Islands

Organismal traits interact with environmental variation to mediate how species respond to shared landscapes. Thus, differences in traits related to dispersal ability or physiological tolerance may result in phylogeographic discordance among co‐distributed taxa, even when they are responding to common barriers. We quantified climatic suitability and stability, and phylogeographic divergence within three reed frog species complexes across the Guineo‐Congolian forests and Gulf of Guinea archipelago of Central Africa to investigate how they responded to a shared climatic and geological history. Our species‐specific estimates of climatic suitability through time are consistent with temporal and spatial heterogeneity in diversification among the species complexes, indicating that differences in ecological breadth may partly explain these idiosyncratic patterns. Likewise, we demonstrated that fluctuating sea levels periodically exposed a land bridge connecting Bioko Island with the mainland Guineo‐Congolian forest and that habitats across the exposed land bridge likely enabled dispersal in some species, but not in others. We did not find evidence that rivers are biogeographic barriers across any of the species complexes. Despite marked differences in the geographic extent of stable climates and temporal estimates of divergence among the species complexes, we recovered a shared pattern of intermittent climatic suitability with recent population connectivity and demographic expansion across the Congo Basin. This pattern supports the hypothesis that genetic exchange across the Congo Basin during humid periods, followed by vicariance during arid periods, has shaped regional diversity. Finally, we identified many distinct lineages among our focal taxa, some of which may reflect incipient or unrecognized species.     

Evolutionary response of cold-adapted chasmophytic plants to Quaternary climatic oscillations in the Mountains of Central Asia (a world hotspot of biodiversity)

Aim

Past climatic oscillations are the main driving force of evolutionary changes in alpine species. Species' response to paleoclimatic oscillations is crucial in forecasting their future response in face of climate warming. The aim of this research is to explore the effect of climatic fluctuations on the evolutionary history, demography, and distribution of high-mountain bellflowers (Campanula lehmanniana complex), the flagship and taxonomically problematic members of chasmophytic vegetation within an underexplored biodiversity hotspot, the Mountains of Central Asia.

Location

Central Asia (Tian Shan, Alai and Zeravshan-Hissar Mountains).

Methods

We used molecular data (ITS, cpDNA, DArTseq-based SNPs) of 262 individuals (70 for the phylogeny reconstruction, and 247 from 31 localities for population studies). We analysed the data using phylogenetic and molecular clock reconstructions, coalescent simulations, and ecological niche modelling.

Results

Tertiary isolation between the Tian-Shanian and Pamir-Alaian populations led to the differentiation of the two main lineages (~5–6 Mya) corresponding to C. eugeniae and C. lehmanniana, whereas further Quaternary isolation into subregions led to intraspecific genetic differentiation, which starts almost simultaneously for both species (~2.7–1.5 Mya). The relatively small genetic admixture among populations indicates rare historic events of connectivity. In response to Holocene warming, the analysed species experienced a substantial decline in effective population size. Currently, the distribution of both taxa is highly influenced by precipitation in the coldest and driest quarters.

Main Conclusions

Our results highlight a general principle that glacial–interglacial cycles and contemporary island-like habitats distribution, shape the genomic variation of high-mountain species. The similar declining demographic trend of examined taxa may suggest the overall response to ongoing climate warming. The results underline also the urgent need for conservation action in alpine regions to preserve their biodiversity.