Italy as a major Ice Age refuge area for the bat Myotis myotis (Chiroptera: Vespertilionidae) in Europe

The distribution of biota from the temperate regions changed considerably during the climatic fluctuations of the Quaternary. This is especially true for many bat species that depend on warm roosts to install their nursery colonies. Surveys of genetic variation among European bats have shown that the southern peninsulas (Iberia and the Balkans) harbour endemic diversity, but to date, no such surveys have been conducted in the third potential glacial refuge area, the Apennine peninsula. We report here the phylogeographical analysis of 115 greater mouse-eared bats ( Myotis myotis ) sampled throughout Italy, and show that 15 of the 18 different haplotypes found in the mitochondrial control region of these bats were unique to the Apennine peninsula. Colonies within this region also showed substantial genetic structure at both mitochondrial ( Φ_ST  = 0.47, P  < 0.001) and nuclear markers ( F _ST = 0.039, P  < 0.001). Based on a comprehensive survey of 575 bats from Europe, these genetic markers further indicate that central Italian populations of M. myotis are more closely related to Greek samples from across the Adriatic Sea, than to other Italian bats. Mouse-eared bat populations from the Apennine peninsula thus represent a complex mixture of several endemic lineages, which evolved in situ , with others that colonized this region more recently along an Adriatic route. Our broad survey also confirms that the Alps represent a relatively impermeable barrier to gene flow for Apennine lineages, even for vagile animals such as bats. These results underline the conservation value of bats from this region and the need to include the Apennine peninsula in phylogeographical surveys in order to provide a more accurate view of the evolution of bats in Europe.     

Evolutionary drivers of phylogeographical diversity in the highlands of Mexico: a case study of the Crotalus triseriatus species group of montane rattlesnakes

Aim To assess the genealogical relationships of widespread montane rattlesnakes in the Crotalus triseriatus species group and to clarify the role of Late Neogene mountain building and Pleistocene pine–oak forest fragmentation in driving the diversification of Mexican highland taxa. Location Highlands of mainland Mexico and the south‐western United States (Texas, New Mexico, and Arizona). Methods A synthesis of inferences was used to address several associated questions about the biogeography of the Mexican highlands and the evolutionary drivers of phylogeographical diversity in co‐distributed taxa. We combined extensive range‐wide sampling (130 individuals representing five putative species) and mixed‐model phylogenetic analyses of 2408 base pairs of mitochondrial DNA to estimate genealogical relationships and divergence times within the C. triseriatus species group. We then assessed the tempo of diversification using a maximum likelihood framework based on the birth–death process. Estimated times of divergences provided a probabilistic temporal component and questioned whether diversification rates have remained constant or varied over time. Finally, we looked for phylogeographical patterns in other co‐distributed taxa. Results We identified eight major lineages within the C. triseriatus group, and inferred strong correspondence between maternal and geographic history within most lineages. At least one cryptic species was detected. Relationships among lineages were generally congruent with previous molecular studies, with differences largely attributable to our expanded taxonomic and geographic sampling. Estimated divergences between most major lineages occurred in the Late Miocene and Pliocene. Phylogeographical structure within each lineage appeared to have been generated primarily during the Pleistocene. Although the scale of genetic diversity recognized affected estimated rates of diversification, rates appeared to have been constant through time. Main conclusions The biogeographical history of the C. triseriatus group implies a dynamic history for the highlands of Mexico. The Neogene formation of the Transvolcanic Belt appears responsible for structuring geographic diversity among major lineages. Pleistocene glacial–interglacial climatic cycles and resultant expansions and contractions of the Mexican pine–oak forest appear to have driven widespread divergences within lineages. Climatic change, paired with the complex topography of Mexico, probably produced a myriad of species‐specific responses in co‐distributed Mexican highland taxa. The high degree of genetic differentiation recovered in our study and others suggests that the Mexican highlands may contain considerably more diversity than currently recognized.     

Phylogeography of Middle American gophersnakes: mixed responses to biogeographical barriers across the Mexican Transition Zone

Aim We used inferences of phylogeographical structure and estimates of divergence times for three species of gophersnakes (Colubridae: Pituophis) distributed across the Mexican Transition Zone (MTZ) to evaluate the postulated association of three Neogene geological events (marine seaway inundation of the Isthmus of Tehuantepec, formation of the Transvolcanic Belt across central Mexico, and secondary uplifting of the Sierra Madre Occidental) and of Pleistocene climate change with inter‐ and intraspecific diversification. Location Mexico, Guatemala, and the western United States. Methods We combined range‐wide sampling (67 individuals representing three putative species distributed across northern Middle America and western North America) and phylogenetic analyses of 1637 base pairs of mitochondrial DNA to estimate genealogical relationships and divergence times. The hypothesized concordance of inferred gene trees with geological histories was assessed using topology tests. Results We identified three major lineages of Middle American gophersnakes, and strong phylogeographical structure within each lineage. Gene trees were statistically congruent with hypothesized geological histories for two of the three postulated geological events. Estimated divergence dates and the geographical distribution of genetic variation further support mixed responses to these geological events. Considerable phylogeographical structure appears to have been generated during the Pleistocene. Main conclusions Phylogenetic and phylogeographical structure in gophersnakes distributed across northern Middle America and western North America highlights the influence of both Neogene vicariance events and Pleistocene climate change in shaping genetic diversity in this region. Despite the presence of two major geographical barriers in southern Mexico, extreme geological and environmental heterogeneity in this area may have differentially structured genetic diversity in highland taxa. To the north, co‐distributed taxa may display a more predictable pattern of diversification across the warm desert regions. Future studies should incorporate nuclear data to disentangle inferred lineage boundaries and further elucidate patterns of mitochondrial introgression.     

Higher genetic diversity in recolonized areas than in refugia of Alnus glutinosa triggered by continent‐wide lineage admixture

Genetic admixture is supposed to be an important trigger of species expansions because it can create the potential for selection of genotypes suitable for new climatic conditions. Up until now, however, no continent‐wide population genetic study has performed a detailed reconstruction of admixture events during natural species expansions. To fill this gap, we analysed the postglacial history of Alnus glutinosa, a keystone species of European swamp habitats, across its entire distribution range using two molecular markers, cpDNA and nuclear microsatellites. CpDNA revealed multiple southern refugia located in the Iberian, Apennine, Balkan and Anatolian Peninsulas, Corsica and North Africa. Analysis of microsatellites variation revealed three main directions of postglacial expansion: (i) from the northern part of the Iberian Peninsula to Western and Central Europe and subsequently to the British Isles, (ii) from the Apennine Peninsula to the Alps and (iii) from the eastern part of the Balkan Peninsula to the Carpathians followed by expansion towards the Northern European plains. This challenges the classical paradigm that most European populations originated from refugial areas in the Carpathians. It has been shown that colonizing lineages have met several times and formed secondary contact zones with unexpectedly high population genetic diversity in Central Europe and Scandinavia. On the contrary, limited genetic admixture in southern refugial areas of A. glutinosa renders rear‐edge populations in the Mediterranean region more vulnerable to extinction due to climate change.     

Phylogeographic structuring and volant mammals: the case of the pallid bat (Antrozous pallidus)

Aim To examine the phylogeographic pattern of a volant mammal at the continental scale. The pallid bat (Antrozous pallidus) was chosen because it ranges across a zone of well‐studied biotic assemblages, namely the warm deserts of North America. Location The western half of North America, with sites in Mexico, the United States, and Canada. Methods PCR amplification and sequencing of the mitochondrial control region was performed on 194 pallid bats from 36 localities. Additional sequences at the cytochrome‐b locus were generated for representatives of each control‐region haplotype. modeltest was used to determine the best set of parameters to describe each data set, which were incorporated into analyses using paup *. Statistical parsimony and measurements of population differentiation (amova , F_ST) were also used to examine patterns of genetic diversity in pallid bats. Results We detected three major lineages in the mitochondrial DNA of pallid bats collected across the species range. These three major clades have completely non‐overlapping geographic ranges. Only 6 of 80 control‐region haplotypes were found at more than a single locality, and sequences at the more conserved cytochrome‐b locus revealed 37 haplotypes. Statistical parsimony generated three unlinked networks that correspond exactly to clades defined by the distance‐based analysis. On average there was c. 2% divergence for the combined mitochondrial sequences within each of the three major clades and c. 7% divergence between each pair of clades. Molecular clocks date divergence between the major clades at more than one million years, on average, using the faster rates, and at more than three million years using more conservative rates of evolution. Main conclusions Divergent haplotypic lineages with allopatric distributions suggest that the pallid bat has responded to evolutionary pressures in a manner consistent with other taxa of the American southwest. These results extend the conclusions of earlier studies that found the genetic structuring of populations of some bat species to show that a widespread volant species may comprise a set of geographically replacing monophyletic lineages. Haplotypes were usually restricted to single localities, and the clade showing geographic affinities to the Sonoran Desert contained greater diversity than did clades to the east and west. While faster molecular clocks would allow for glacial cycles of the Pleistocene as plausible agents of diversification of pallid bats, evidence from co‐distributed taxa suggests support for older events being responsible for the initial divergence among clades.     

Testing the efficiency of nested barriers to dispersal in the Mediterranean high mountain plant Edraianthus graminifolius (Campanulaceae)

Due to strong spatial heterogeneity and limited Pleistocene glaciation, the Balkan Peninsula is a major European biodiversity hot spot. Surprisingly little, however, is known about patterns and processes of intraspecific diversification of its biota in general and of high‐altitude species in particular. A well‐suited system to test hypotheses with respect to various isolating factors acting at different geographic scales and to explore full‐range phylogeographic patterns on the Balkan Peninsula is Edraianthus graminifolius (Campanulaceae), distributed in the western Balkan mountain systems, the southwestern Carpathians and the Apennine Peninsula. To this end, we used a dense population sampling and employed amplified fragment length polymorphism (AFLP) markers and plastid DNA sequences supplemented by ecological niche modelling. The strongest splits were inferred to separate southern and northern Balkan populations from the central ones, from where range extension occurred to the Carpathians and, in more recent times, once or twice to the Apennine Peninsula. The three genetic groups in the western Balkan Peninsula were remarkably congruent among molecular markers, suggesting that the barriers to gene flow acted over long time periods facilitating allopatric differentiation. Each main group of Balkan populations contained genetically and geographically distinct subgroups, which likely are the result of local refugia during warmer periods. Evidently, the topographically highly complex and during the Last Glacial Maximum only locally glaciated Balkan Peninsula is a hot spot of species richness and endemism as well as a sanctuary of intraspecific genetic diversity, even if the underlying causes remain insufficiently understood.     

Phylogenetic analyses of Gammaridae crustacean reveal different diversification patterns among sister lineages in the Tethyan region

The Gammaridae shows the greatest disparity in species diversity and distribution pattern in the Amphipoda, with some genera ranging from the Palearctic to Nearctic, while others are limited to the Mediterranean region or ancient Tethyan margins. Here we present the first molecular phylogenetic analysis of the Gammaridae to investigate its evolutionary history using four genetic markers and a comprehensive set of taxa representing 198 species. The phylogenetic results revealed that the Gammaridae originated from the Tethyan region in the Cretaceous, and split into three morphologically and geographically distinct lineages by the end of the Paleocene. Diversification analysis combined with paleogeological evidence suggested that the Tethyan changes induced by sea‐level fluctuation and tectonic uplift triggered different diversification modes and range expansions for the three lineages. The Gammarus lineage underwent an early rapid radiation across Eurasia and North America, then declined towards modern species. Pontogammarids maintained stable diversification with restricted distributions around the Tethyan basin, whereas sarothrogammarids experienced evolutionary stasis by stranding on the ancient Tethyan margins. Our findings suggest that environmental changes have played an important role in the diversification of Gammaridae lineages, which could be an opportunity to promote adaptive radiations in new habitats, or constraints resulting in evolutionary relicts.     

A combined genetic-morphometric analysis unravels the complex biogeographical history of Polyommatus icarus and Polyommatus celina common blue butterflies

Widespread species have the potential to reveal large‐scale biogeographical patterns, as well as responses to environmental changes possibly unique to habitat generalists. This study presents a continental‐scale phylogeographical analysis of Polyommatus icarus, one of the most common Palaearctic butterflies, and the morphologically and ecologically similar Polyommatus celina, a recently discovered cryptic species. By combining data from mitochondrial [cytochrome c oxidase subunit I (COI)] and nuclear [internal transcribed spacer (ITS2)] molecular markers with geometric morphometrics, we document a complex phylogeographical history for the two species. Despite morphological similarities, the genetic divergence between these two species is high (more than 5% at COI) and they are not sister species. For the first time, we show that P. celina occurs not only in North Africa but also in Europe, where it inhabits several west Mediterranean islands, as well as large parts of Iberia, where it occurs in parapatry with P. icarus. The two species appear to completely exclude each other on islands, but we provide morphological and molecular evidence that introgression occurred in the Iberian Peninsula. We discovered strongly diverged lineages that seem to represent relict populations produced by past range expansions and contractions: Crete and Iberian isolates for P. icarus, Balearics–Sardinia and Sicily–Lipari for P. celina. This study shows that a combined genetic‐morphometric approach can shed light on cryptic diversity while providing the necessary resolution to reconstruct a fine‐scale phylogeographical history of species at both spatial and temporal levels.     

Geological habitat template overrides late Quaternary climate change as a determinant of range dynamics and phylogeography in some habitat‐specialist water beetles

Aim We investigated the roles of lithology and climate in constraining the ranges of four co‐distributed species of Iberian saline‐habitat specialist water beetles (Ochthebius glaber, Ochthebius notabilis, Enochrus falcarius and Nebrioporus baeticus) across the late Quaternary and in shaping their geographical genetic structure. The aim was to improve our understanding of the effects of past climate changes on the biota of arid Mediterranean environments and of the relative importance of history and landscape on phylogeographical patterns. Location Iberian Peninsula, Mediterranean. Methods We combined species distribution modelling (SDM) and comparative phylogeography. We used a multi‐model inference and model‐averaging approach both for assessment of range determinants (climate and lithology) and for provision of spatially explicit estimates of the species current and Last Glacial Maximum (LGM) potential ranges. Potential LGM distributions were then contrasted with the phylogeographical and population expansion patterns as assessed using mitochondrial DNA sequence data. We also evaluated the relative importance of geographical distance, habitat resistance and historical isolation for genetic structure in a causal modelling framework. Results Lithology poses a strong constraint on the distribution of Iberian saline‐habitat specialist water beetles, with a variable, but generally moderate, additional influence by climate. The degree to which potential LGM distributions were reduced and fragmented decreased with increasing importance of lithology. These SDM‐based suitability predictions were mostly congruent with phylogeographical and population genetic patterns across the study species, with stronger geographical structure in the genetic diversity of the more temperature‐sensitive species (O. glaber and E. falcarius). Furthermore, while historical isolation was the only factor explaining genetic structure in the more temperature‐sensitive species, lithology‐controlled landscape configuration also played an important role for those species with more lithology‐determined ranges (O. notabilis and N. baeticus). Main conclusions Our data show that lithology is an important constraint on the distribution and range dynamics of endemic Iberian saline‐habitat water beetles, in interaction with climate and long‐term climate change, and overrides the latter in importance for some species. Hence, geological landscape structure and long‐term history may codetermine the overall range and the distribution of genetic lineages in endemic species with specialized edaphic requirements.     

Testing phylogenetic hypotheses for reconstructing the evolutionary history of Dolichopoda cave crickets in the eastern Mediterranean

Aim To investigate the molecular phylogenetic divergence and historical biogeography of cave crickets belonging to the genus Dolichopoda (Orthoptera, Rhaphidophoridae). Location Caves in continental and insular Greece. Methods We sequenced 1967 bp of mitochondrial DNA, corresponding to three fragments of the small and large subunit of the ribosomal RNA (16S and 12S rRNA, respectively) and to the subunit I of cytochrome oxidase (COI), to reconstruct phylogenetic relationships among all 30 known Greek species of Dolichopoda. Alternative hypotheses about the colonization of the Hellenic Peninsula by Dolichopoda species were tested by comparing the degree of discordance between species trees and gene trees under four plausible biogeographical scenarios. Results The present study revealed a rather well resolved phylogeny at species level, identifying a number of clades that represent long‐separated lineages and diverse evolutionary histories within the genus Dolichopoda. Two main clades were revealed within Hellenic–Aegean species, identifying a north‐western and a south‐eastern species group. Based on Bayesian analysis, we applied a relaxed molecular clock to estimate the divergence times between the lineages. The results revealed that the origins of eastern Mediterranean lineages are much older than those of previously studied western Mediterranean Dolichopoda. Tests of alternative biogeographical hypotheses showed that a double colonization of the Hellenic Peninsula, following separate continental and trans‐Aegean routes during the Messinian stage, best accounts for the present distribution of Greek Dolichopoda species. Main conclusions Reconstruction and biogeographical hypothesis testing indicated that the colonization of Greece by Dolichopoda species comprised two episodes and two different routes. The southern lineage probably arose from a trans‐Aegean colonization during the Messinian salinity crisis (5.96–5.33 Ma). The northern lineage could be the result of dispersal from the north through the Balkan Peninsula. The opening of the Mid‐Aegean Trench could have promoted an initial diversification within the uprising Anatolian Plateau, while the Messinian marine regression offered the conditions for a rapid dispersal through the whole Aegean–Hellenic region. In addition, climatic events during the Plio‐Pleistocene may have been responsible for the speciation within each of the two different phylogeographical units, principally attributable to vicariance events.     

Contrasting phylogeography of two Western Palaearctic fish parasites despite similar life cycles

Aim

We used comparative phylogeography of two intestinal parasites of freshwater fish to test whether similarity in life cycle translates into concordant phylogeographical history. The thorny‐headed worms Pomphorhynchus laevis and P. tereticollis (Acanthocephala) were formerly considered as a single species with a broad geographical and host range within the Western Palaearctic.

Location

Central and eastern parts of Northern Mediterranean area, Western and Central Europe, Ponto‐Caspian Europe.

Methods

A mitochondrial marker (COI) was sequenced for 111 P. laevis and 50 P. tereticollis individuals and nuclear ITS1 and ITS2 sequences were obtained for 37 P. laevis and 21 P. tereticollis. Genetic divergence, phylogenetic relationships and divergence time were estimated for various lineages within each species, and their phylogeographical patterns were compared to known palaeogeographical events in Western Palaearctic. Biogeographical histories of each species were inferred.

Results

The two species show very different phylogeographical patterns. Five lineages were identified in P. laevis, partially matching several major biogeographical regions defined in the European riverine fish fauna. The early stages of P. laevis diversification occurred in the peri‐Mediterranean area, during the Late Miocene. Subsequent expansion across Western Europe and Russia was shaped by dispersal and vicariant events, from Middle Pliocene to Middle Pleistocene. By contrast, P. tereticollis has differentiated more recently within the Western and Central parts of Europe, and shows weak geographical and genetic structuring.

Conclusion

Our study highlights weak to moderate similarity in the phylogeographical pattern of these acanthocephalan parasites compared to their amphipod and fish hosts. The observed differences in the timing of dispersion and migration routes taken may reflect the use of a range of final hosts with different ecologies and dispersal capabilities. By using a group underrepresented in phylogeographical studies, our study is a valuable contribution to revealing the biogeography of host–parasite interactions in continental freshwaters.     

Insights into historical drainage evolution based on the phylogeography of the chevron snakehead fish (Channa striata) in the Mekong Basin

1. The phylogeography of freshwater taxa is often integrally linked with landscape changes such as drainage re‐alignments that may present the only avenue for historical dispersal for these taxa. Classical models of gene flow do not account for landscape changes and so are of little use in predicting phylogeography in geologically young freshwater landscapes. When the history of drainage formation is unknown, phylogeographical predictions can be based on current freshwater landscape structure, proposed historical drainage geomorphology, or from phylogeographical patterns of co‐distributed taxa. 2. This study describes the population structure of a sedentary freshwater fish, the chevron snakehead (Channa striata), across two river drainages on the Indochinese Peninsula. The phylogeographical pattern recovered for C. striata was tested against seven hypotheses based on contemporary landscape structure, proposed history and phylogeographical patterns of co‐distributed taxa. 3. Consistent with the species ecology, analysis of mitochondrial and microsatellite loci revealed very high differentiation among all sampled sites. A strong signature of historical population subdivision was also revealed within the contemporary Mekong River Basin (MRB). Of the seven phylogeographical hypotheses tested, patterns of co‐distributed taxa proved to be the most adequate for describing the phylogeography of C. striata. 4. Results shed new light on SE Asian drainage evolution, indicating that the Middle MRB probably evolved via amalgamation of at least three historically independent drainage sections and in particular that the Mekong River section centred around the northern Khorat Plateau in NE Thailand was probably isolated from the greater Mekong for an extensive period of evolutionary time. In contrast, C. striata populations in the Lower MRB do not show a phylogeographical signature of evolution in historically isolated drainage lines, suggesting drainage amalgamation has been less important for river landscape formation in this region.     

Geographic genetic structure of Iberian columbines (gen. <Emphasis Type="Italic">Aquilegia</Emphasis>)

Southern European columbines (genus Aquilegia) are involved in active processes of diversification, and the Iberian Peninsula offers a privileged observatory to witness the process. Studies on Iberian columbines have provided significant advances on species diversification, but we still lack a complete perspective of the genetic diversification in the Iberian scenario. This work explores how genetic diversity of the genus Aquilegia is geographically structured across the Iberian Peninsula. We used Bayesian clustering methods, principal coordinates analyses, and NJ phenograms to assess the genetic relationships among 285 individuals from 62 locations and detect the main lineages. Genetic diversity of Iberian columbines consists of five geographically structured lineages, corresponding to different Iberian taxa. Differentiation among lineages shows particularly complex admixture patterns at Northeast and highly homogeneous toward Northwest and Southeast. This geographic genetic structure suggests the existence of incomplete lineage sorting and interspecific hybridization as could be expected in recent processes of diversification under the influence of quaternary postglacial migrations. This scenario is consistent with what is proposed by the most recent studies on European and Iberian columbines, which point to geographic isolation and divergent selection by habitat specialization as the main diversification drivers of the Iberian Aquilegia complex.     

Phylogeography of a subalpine tall‐herb Ranunculus platanifolius (Ranunculaceae) reveals two main genetic lineages in the European mountains

A phylogeographical analysis of Ranunculus platanifolius, a typical European subalpine tall‐herb species, indicates the existence of two main genetic lineages based on amplified fragment length polymorphism (AFLP) markers. One group comprises populations from the Balkan Peninsula and the south‐eastern Carpathians and the other includes the remaining part of the range of the species, encompassing the western Carpathians, Sudetes, Alps, Pyrenees and Scandinavia. The main phylogeographical break observed in this species runs across the Carpathians and separates the main parts of this range (western and south‐eastern Carpathians), supporting a distinct glacial history of populations in these areas. The high genetic similarity of the Balkan Peninsula and south‐eastern Carpathian populations could indicate a common glacial refugium for these contemporarily isolated areas of species distribution. The western and northern part of the species range displays an additional weak differentiation into regional phylogeographical groups, which could have been shaped by isolation in glacial refugia or even by a postglacial isolation. The observed weak phylogeographical structure could also be linked with ecological requirements, allowing survival along streams in relatively low, forested mountain ranges. © 2013 The Linnean Society of London     

Alpine crossroads or origin of genetic diversity? Comparative phylogeography of two sympatric microgastropod species

The Alpine Region, constituting the Alps and the Dinaric Alps, has played a major role in the formation of current patterns of biodiversity either as a contact zone of postglacial expanding lineages or as the origin of genetic diversity. In our study, we tested these hypotheses for two widespread, sympatric microgastropod taxa--Carychium minimum O.F. Müller, 1774 and Carychium tridentatum (Risso, 1826) (Gastropoda, Eupulmonata, Carychiidae)--by using COI sequence data and species potential distribution models analyzed in a statistical phylogeographical framework. Additionally, we examined disjunct transatlantic populations of those taxa from the Azores and North America. In general, both Carychium taxa demonstrate a genetic structure composed of several differentiated haplotype lineages most likely resulting from allopatric diversification in isolated refugial areas during the Pleistocene glacial periods. However, the genetic structure of Carychium minimum is more pronounced, which can be attributed to ecological constraints relating to habitat proximity to permanent bodies of water. For most of the Carychium lineages, the broader Alpine Region was identified as the likely origin of genetic diversity. Several lineages are endemic to the broader Alpine Region whereas a single lineage per species underwent a postglacial expansion to (re)colonize previously unsuitable habitats, e.g. in Northern Europe. The source populations of those expanding lineages can be traced back to the Eastern and Western Alps. Consequently, we identify the Alpine Region as a significant 'hot-spot' for the formation of genetic diversity within European Carychium lineages. Passive dispersal via anthropogenic means best explains the presence of transatlantic European Carychium populations on the Azores and in North America. We conclude that passive (anthropogenic) transport could mislead the interpretation of observed phylogeographical patterns in general.     

The discordance of diversification: evolution in the tropical‐montane frogs of the Eastern Arc Mountains of Tanzania

Species with similar geographical distribution patterns are often assumed to have a shared biogeographical history, an assumption that can be tested with a combination of molecular, spatial, and environmental data. This study investigates three lineages of Hyperolius frogs with concordant ranges within the Eastern Afromontane Biodiversity Hotspot to determine whether allopatric populations of co‐distributed lineages shared a parallel biogeographical response to their shared paleoclimatic histories. The roles of refugial distributions, isolation, and climate cycles in shaping their histories are examined through Hierarchical Approximate Bayesian Computation, comparative phylogeography, and comparisons of current and past geographical distributions using ecological niche models. Results from these analyses show these three lineages to have independent evolutionary histories, which current spatial configurations of sparsely available habitat (montane wetlands) have moulded into convergent geographical ranges. In spite of independent phylogeographical histories, diversification events are temporally concentrated, implying that past vicariant events were significant at the generic level. This mixture of apparently disparate histories is likely due to quantifiably different patterns of expansion and retreat among species in response to past climate cycles. Combining climate modelling and phylogeographical data can reveal unrecognized complexities in the evolution of co‐distributed taxa.     

Hybridization and introgression in Carex aquatilis and C. paleacea

The diversification and distribution of Abies species throughout the Mediterranean region has led to a complex of species which are difficult to classify. An open question is whether these mainly allopatric taxa have exchanged genetic information via secondary contact. We studied the variation and geographic distribution of paternally inherited chloroplast DNA markers in nine Mediterranean Abies taxa. Markers with high and low mutation rates were applied in order to differentiate among a scenario of secondary genetic contact and a scenario of complete isolation after speciation. The observed molecular variation was analysed using statistical parsimony, geostatistics, and measures of population genetic differentiation. Ancient paternal lineages, represented by markers with low mutation rates, were shared among species. The central and widespread A. alba retained all ancient lineages whereas other species exhibited fewer, down to a single lineage. In contrast, modern lineages, depicted by markers with high mutation rates, were largely separated among species. The western Mediterranean A. pinsapo and A. numidica were clearly separated from each other and from the remaining Abies species. This indicates the absence of secondary contact. The same scenario applies to the eastern Mediterranean Abies species. An exception is the parapatric complex of A. alba, A. cephalonica, and their supposed hybrid A. borisii regis, which exhibited evidence of secondary contact.     

Contrasting patterns of historical colonization in white oaks (Quercus spp.) in California and Europe

Phylogeography allows the inference of evolutionary processes that have shaped the current distribution of genealogical lineages across a landscape. In this perspective, comparative phylogeographical analyses are useful in detecting common historical patterns by either comparing different species within the same area within a continent or by comparing similar species in different areas. Here, we analyse one taxon (the white oak, genus Quercus, subgenus Quercus, section Quercus) that is widespread worldwide, and we evaluate its phylogeographical pattern on two different continents: western North America and Western Europe. The goals of the present study are: (i) to compare the chloroplast genetic diversity found in one California oak species vs. that found in the extensively studied European oak species (in France and the Iberian Peninsula); (ii) to contrast the geographical structure of haplotypes between these two taxa and test for a phylogeographical structure for the California species. For this purpose, we used the same six maternally inherited chloroplast microsatellite markers and a similar sampling strategy. The haplotype diversity within site as well as the differentiation among sites was alike in both taxa, but the Californian species has higher allelic richness with a greater number of haplotypes (39 vs. 11 in the European white oak complex). Furthermore, in California these 39 haplotypes are distributed locally in patches while in the European oaks haplotypes are distributed into lineages partitioned longitudinally. These contrasted patterns could indicate that gene movement in California oak populations have been more stable in response to past climatic and geological events, in contrast to their European counterparts.     

The Great American Interchange in birds: a phylogenetic perspective with the genus Trogon

The 'Great American Interchange' (GAI) is recognized as having had a dramatic effect on biodiversity throughout the Neotropics. However, investigation of patterns in Neotropical avian biodiversity has generally been focused on South American taxa in the Amazon Basin, leaving the contribution of Central American taxa under-studied. More rigorous studies of lineages distributed across the entire Neotropics are needed to uncover phylogeographical patterns throughout the area, offering insights into mechanisms that contribute to overall Neotropical biodiversity. Here we use mitochondrial DNA sequence data and intensive geographical sampling from the widespread Neotropical avian genus Trogon to investigate the role of the GAI in shaping its phylogeographical history. Our results show that genetic diversity in Trogon exceeds the perceived biodiversity, and that the GAI resulted in lineage diversification within the genus. Despite greater diversity in South America, a Central American centre of origin with multiple and independent dispersals into South America is indicated. These dispersals were followed by the evolution of divergent lineages associated with the Andes Mountains and other South American geographical features. According to our phylogenetic reconstructions, several species, which were originally defined by morphological characters, are nonmonophyletic. In sum, our results elucidate the evolutionary history of Trogon , reveal patterns obscured by extant biodiversity, and serve as a biogeographical model to consider in future studies.