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Background In contrast to the Western Palearctic and Nearctic biogeographic regions, the phylogeography of Eastern-Palearctic terrestrial vertebrates has received relatively little attention. In East Asia, tectonic events, along with Pleistocene climatic conditions, likely affected species distribution and diversity, especially through their impact on sea levels and the consequent opening and closing of land-bridges between Eurasia and the Japanese Archipelago. To better understand these effects, we sequenced mitochondrial and nuclear markers to determine phylogeographic patterns in East-Asian tree frogs, with a particular focus on the widespread H. japonica . Results We document several cryptic lineages within the currently recognized H. japonica populations, including two main clades of Late Miocene divergence (~5 Mya). One occurs on the northeastern Japanese Archipelago (Honshu and Hokkaido) and the Russian Far-East islands (Kunashir and Sakhalin), and the second one inhabits the remaining range, comprising southwestern Japan, the Korean Peninsula, Transiberian China, Russia and Mongolia. Each clade further features strong allopatric Plio-Pleistocene subdivisions (~2-3 Mya), especially among continental and southwestern Japanese tree frog populations. Combined with paleo-climate-based distribution models, the molecular data allowed the identification of Pleistocene glacial refugia and continental routes of postglacial recolonization. Phylogenetic reconstructions further supported genetic homogeneity between the Korean H. suweonensis and Chinese H. immaculata , suggesting the former to be a relic population of the latter that arose when the Yellow Sea formed, at the end of the last glaciation. Conclusions Patterns of divergence and diversity were likely triggered by Miocene tectonic activities and Quaternary climatic fluctuations (including glaciations), causing the formation and disappearance of land-bridges between the Japanese islands and the continent. Overall, this resulted in a ring-like diversification of H. japonica around the Sea of Japan. Our findings urge for important taxonomic revisions in East-Asian tree frogs. First, they support the synonymy of H. suweonensis (Kuramoto, 1980) and H. immaculata (Boettger, 1888). Second, the nominal H. japonica (Günther, 1859) represents at least two species: an eastern (new taxon A) on the northern Japanese and Russian Far East islands, and a southwestern species (n. t. B) on southern Japanese islands and possibly also forming continental populations. Third, these continental tree frogs may also represent an additional entity, previously described as H. stepheni Boulenger, 1888 (senior synonym of H. ussuriensis Nikolskii, 1918). A complete revision of this group requires further taxonomic and nomenclatural analyses, especially since it remains unclear to which taxon the species-epitheton japonica corresponds to.

Mountains, representing storehouses of biodiversity, endemism and threatened species, are biodiversity hotspots of great conservation importance. However, increasing evidence indicates that mountain species throughout the world are responding to climate change, past or contemporary, by shifting their geographic distributions and patterns of genetic diversity, potentially affecting their adaptive capacity and increasing risk of extinction. Using the iconic high‐elevation frog Nanorana parkeri as indicator, we showed how spatial analyses of climatic stability combined with genetic data allow unravelling amphibian responses to past and future climate changes on ‘the roof of the world’—the Qinghai‐Tibetan Plateau. We found that areas along the Yarlung Tsangpo Valley were climatically more stable relative to other regions, apparently serving as a large climatic refugium during Quaternary glaciations, but that these areas will likely be affected by future climate change. As populations closer to Quaternary refugia usually had higher genetic diversity, current genetic diversity can be explained in the largest part by distance to historically stable areas, outweighing other historical and contemporary factors. Along with the dynamics of suitable range, a fluctuating habitat fragmentation supported the pattern of historical changes in genetic diversity (Ne) over time. Our results emphasize strong relationships between amphibian genetic diversity, past range dynamics and where to preserve suitable habitats in the face of future climate changes. More generally, our findings highlighted a central role of refugia during Quaternary climatic fluctuations, and how isolation from refugia may have modulated amphibian genetic diversity across the Qinghai‐Tibetan Plateau. Given substantially underestimated genetic diversity and endemism of amphibians, ever‐accelerating environmental changes on the Qinghai‐Tibetan Plateau could induce severe loss of unique diversity. The authors assess the extent to which Quaternary climate fluctuations can explain variation in population genetic diversity and unravelling future responses to climate changes for the Tibetan frog. The findings have important implications for conservation of amphibians world‐wide under ongoing and expected environment change.

Aim Species diversity in the region of the Qinghai–Tibet Plateau has been extensively explored, whereas the distribution of genetic diversity remains poorly understood in this species‐rich area, parts of which are listed as biodiversity hotspots. In this study, we aimed to map the patterns of genetic diversity and divergence of plant species in this region, and to identify potential evolutionary hotspots for conservation planning. Location Region of the Qinghai–Tibet Plateau (QTP). Methods We compiled published molecular data for 60 plant species, and calculated intra‐population genetic diversity and inter‐population genetic divergence using haplotype sequences (chloroplast or mitochondrial DNA). We analysed the relationships between genetic diversity and longitude, latitude and elevation. We mapped the landscapes of genetic diversity and divergence for each species in GIS, and combined the resulting landscapes in order to identify hotspots of high genetic diversity and divergence. Results There were no significant relationships between genetic diversity and longitude, latitude and elevation. For most species, areas characterized by high genetic diversity and divergence were located across the Hengduan Mountains. Nine evolutionary hotspots across the region of the QTP were identified. Main conclusions The Hengduan Mountains are a remarkable hotspot of all three dimensions of biodiversity (genes, species and ecosystems), yet patterns of genetic diversity were partially incongruent with the distribution of species diversity. For example, several hotspots of genetic diversity were located on the QTP proper, which is relatively species poor. This partial geographic mismatch between species and genetic diversity highlights the need to consider both aspects in conservation programs. Our study suggests that more protected areas in the region of the QTP need to be established in order to protect genetic diversity and thus adaptive potential.

Aim The genus Abies exemplifies plant diversification related to long-term climatic, geological and evolutionary changes. Today, the Mediterranean firs comprise nine species, one natural hybrid and several varieties. Here I summarize current knowledge concerning the origin and evolution of the genus Abies in the Mediterranean Basin and propose a comprehensive hypothesis to explain the isolation and speciation pattern of Mediterranean firs. Location The Mediterranean Basin. Methods The literature on Abies was reviewed, focusing on the morphology, fossil records, molecular ecology, phytosociology and biogeography of the genus in the Mediterranean Basin. Results Abies fossils from the western Mediterranean indicate a wide Tertiary circum-Mediterranean distribution of the Abies ancestor. Palaeogeographical data also suggest a single eastern Mediterranean Tertiary ancestor. Following the Miocene to Pliocene climate crisis and marine transgressions, the ancestor of the northern Mediterranean firs is hypothesized to have separated into two eastern groups, one on the Balkan Peninsula and the other in Asia Minor. However, land bridges may have permitted gene flow at times. A southward migration of A. alba to refugia, where older fir species may have remained isolated since the Miocene, could explain recent findings indicating that morphologically distant species are more closely related than expected based on such morphological classification. Main conclusions The Abies genus appears to have undergone significant morphological differentiation that does not necessarily imply reproductive isolation. That is, long-term Mediterranean Basin dryness along a south-eastern to north-western gradient may have caused an initial Miocene-Pliocene speciation sequence. Pleistocene glacial cycles probably forced migrations to occur, leading to repeated contact between fir species in glacial refugia.

Quaternary palaeopalynological records collected throughout the Iberian Peninsula and species distribution models (SDMs) were integrated to gain a better understanding of the historical biogeography of the Iberian Abies species (i.e. Abies pinsapo and Abies alba). We hypothesize that SDMs and Abies palaeorecords are closely correlated, assuming a certain stasis in climatic and topographic ecological niche dimensions. In addition, the modelling results were used to assign the fossil records to A. alba or A. pinsapo, to identify environmental variables affecting their distribution, and to evaluate the ecological segregation between the two taxa. The Iberian Peninsula. For the estimation of past Abies distributions, a hindcasting process was used. Abies pinsapo and A. alba were modelled individually, first calibrating the model for their current distributions in relation to the present climate, and then projecting it into the past--the last glacial maximum (LGM) and the Middle Holocene periods--in relation to palaeoclimate simulations. The resulting models were compared with Iberian-wide fossil pollen records to detect areas of overlap. The overlap observed between past Abies refugia--inferred from fossil pollen records--and the SDMs helped to construct the Quaternary distribution of the Iberian Abies species. SDMs yielded two well-differentiated potential distributions: A. pinsapo throughout the Baetic mountain Range and A. alba along the Pyrenees and Cantabrian Range. These results propose that the two taxa remained isolated throughout the Quaternary, indicating a significant geographical and ecological segregation. In addition, no significant differences were detected comparing the three projections (present-day, Mid-Holocene and LGM), suggesting a relative climate stasis in the refuge areas during the Quaternary. Our results confirm that SDM projections can provide a useful complement to palaeoecological studies, offering a less subjective and spatially explicit hypothesis concerning past geographic patterns of Iberian Abies species. The integration of ecological-niche characteristics from known occurrences of Abies species in conjunction with palaeoecological studies could constitute a suitable tool to define appropriate areas in which to focus proactive conservation strategies.

Aim: We describe patterns of skull size and shape variation in an Atlantic forest endemic rodent to test the influence of genetic structure, historical and environmental variables upon intraspecific morphological variability. Location: South America, Brazil, Atlantic forest. Methods: We analyse subtle differences in skull morphology of Akodon cursor through geometric morphometrics applied to 324 individuals from 12 localities distributed throughout the species range. Using cytochrome-b gene (cyt-b) sequences from 125 individuals (38 localities), we describe underlying patterns of genetic structure and transform them into distance measures that are included in our morphological analyses. We estimate the relative importance of genetic structure, historical variables and environmental variables on skull size and shape through mixed model selection and Akaike's information criterion. Results: Geographical patterns in skull size are mainly explained by non-random factors related to primary productivity and precipitation, whereas spatial shifts in shape correlate with mitochondrial divergence. Cytochrome-b data revealed a phylogeographic break around the Jequitinhonha River, yet striking morphological shifts were observed further south. Differences in palaeostability between regions, and the configuration of rivers, appear as secondary sources of explanation for observed patterns. Main conclusions: Multiple forces explain morphological variation within A. cursor. Teasing apart the effects of local adaptation and gene flow may be difficult, but is a key to improve our understanding of the drivers of intraspecific morphological variation. Our findings support the view that size is a more labile feature than shape, and that it may more easily break away from constraints imposed by gene flow. The combination of random and non-random factors, together with documented breaks in the distribution of the Atlantic forest over the Late Quaternary, accounts for the majority of morphological differences observed in A. cursor.

Understanding the factors driving the Quaternary distribution of Abies in the Tibetan Plateau (TP) is crucial for biodiversity conservation and for predicting future anthropogenic impacts on ecosystems. Here, we collected Quaternary paleo‐, palynological, and phylogeographical records from across the TP and applied ecological niche models (ENMs) to obtain a profound understanding of the different adaptation strategies and distributional changes in Abies trees in this unique area. We identified environmental variables affecting the different historical biogeographies of four related endemic Abies taxa and rebuilt their distribution patterns over different time periods, starting from the late Pleistocene. In addition, modeling and phylogeographic results were used to predict suitable refugia for Abies forrestii, A. forrestii var. georgei, A. fargesii var. faxoniana, and A. recurvata. We supplemented the ENMs by investigating pollen records and diversity patterns of cpDNA for them. The overall reconstructed distributions of these Abies taxa were dramatically different when the late Pleistocene was compared with the present. All Abies taxa gradually receded from the south toward the north in the last glacial maximum (LGM). The outcomes showed two well‐differentiated distributions: A. fargesii var. faxoniana and A. recurvata occurred throughout the Longmen refuge, a temporary refuge for the LGM, while the other two Abies taxa were distributed throughout the Heqing refuge. Both the seasonality of precipitation and the mean temperature of the driest quarter played decisive roles in driving the distribution of A. fargesii var. faxoniana and A. recurvata, respectively; the annual temperature range was also a key variable that explained the distribution patterns of the other two Abies taxa. Different adaptation strategies of trees may thus explain the differing patterns of distribution over time at the TP revealed here for endemic Abies taxa. All Abies species gradually receded from the south toward the north in the last glacial maximum (LGM). Abies fargesii var. faxoniana and A. recurvata occurred throughout the Longmen refuge, which was a temporary refuge only for the LGM, while the other two Abies taxa were distributed throughout the Heqing refuge. Different adaptation strategies may explain the different patterns of distribution of the four endemic Abies taxa.

North American water shrews, which have traditionally included Sorex alaskanus, S. bendirii, and S. palustris, are widely distributed through Nearctic boreal forests and adapted for life in semiaquatic environments. Molecular mitochondrial signatures for these species have recorded an evolutionary history with variable levels of regional divergence, suggesting a strong role of Quaternary environmental change in speciation processes. We expanded molecular analyses, including more-comprehensive rangewide sampling of specimens representing North American water shrew taxa, except S. alaskanus, and sequencing of 4 independent loci from the nuclear and mitochondrial genomes. We investigated relative divergence of insular populations along the North Pacific Coast, and newly recognized diversity from southwestern montane locations, potentially representing refugial isolates. Congruent independent genealogies, lack of definitive evidence for contemporary gene flow, and high support from coalescent species trees indicated differentiation of 4 major geographic lineages over multiple glacial cycles of the late Quaternary, similar to a growing number of boreal taxa. Limited divergence of insular populations suggested colonization following the last glacial. Characterization of southwestern montane diversity will require further sampling but divergence over multiple loci is indicative of a relictual sky-island fauna. We have reviewed and revised North American water shrew taxonomy including the recognition of 3 species within what was previously known as S. palustris. The possibility of gene flow between most distantly related North American water shrew lineages coupled with unresolved early diversification of this group and other sibling species reflects a complex but potentially productive system for investigating speciation processes.

The Italian and Balkan peninsulas have been places traditionally highlighted as Pleistocene glacial refuges. The Iberian Peninsula, however, has been a focus of controversy between geobotanists and palaeobotanists as a result of its exclusion from this category on different occasions. In the current paper, we synthesise geological, molecular, palaeobotanical and geobotanical data that show the importance of the Iberian Peninsula in the Western Mediterranean as a refugium area. The presence of Aesculus aff. hippocastanum L. at the Iberian site at Cal Guardiola (Tarrasa, Barcelona, NE Spain) in the Lower—Middle Pleistocene transition helps to consolidate the remarkable role of the Iberian Peninsula in the survival of tertiary species during the Pleistocene. The palaeodistribution of the genus in Europe highlights a model of area abandonment for a widely-distributed species in the Miocene and Pliocene, leading to a diminished and fragmentary presence in the Pleistocene and Holocene on the southern Mediterranean peninsulas. Aesculus fossils are not uncommon within the series of Tertiary taxa. Many appear in the Pliocene and suffer a radical impoverishment in the Lower—Middle Pleistocene transition. Nonetheless some of these tertiary taxa persisted throughout the Pleistocene and Holocene up to the present in the Iberian Peninsula. Locating these refuge areas on the Peninsula is not an easy task, although areas characterised by a sustained level of humidity must have played an predominant role.

We describe a new palaeobotanical site at Bubano quarry on the easternmost Po plain, northern Italy. Pollen and macrofossils from river and marsh sediments demonstrate the occurrence of Picea in a Pinus sylvestris forest growing in a radius of some tens of kilometres south of the sedimentation place, at the beginning of the Late-glacial interstadial. The Late-glacial and Holocene history of Picea in the northern Apennines is reconstructed on the basis of the palaeobotanical record. The sharp climatic continentality increase eastwards across the northern Apennines from the Tyrrhenian to the Adriatic coast is considered significant for the survival of Picea during the Late-glacial. The most critical phase of survival is related to the moisture changes and consequent Abies competition associated with the last glacial-interglacial transition and the early Holocene. The residual spruce populations expanded during the middle Holocene. The history of Picea in the northern Apennines is a case of ineffective interglacial spread of tree populations from pre-existing stands of LGM (Last Glacial Maximum) and Late-glacial age.