Comparative phylogeography of unglaciated eastern North America

Regional phylogeographical studies involving co-distributed animal and plant species have been conducted for several areas, most notably for Europe and the Pacific Northwest of North America. Until recently, phylogeographical studies in unglaciated eastern North America have been largely limited to animals. As more studies emerge for diverse lineages (including plants), it seems timely to assess the phylogeography across this region: (i) comparing and contrasting the patterns seen in plants and animals; (ii) assessing the extent of pseudocongruence; and (iii) discussing the potential applications of regional phylogeography to issues in ecology, such as response to climatic change. Unglaciated eastern North America is a large, geologically and topographically complex area with the species examined having diverse distributions. Nonetheless, some recurrent patterns emerge: (i) maritime - Atlantic vs. Gulf Coast; (ii) Apalachicola River discontinuity; (iii) Tombigbee River discontinuity; (iv) the Appalachian Mountain discontinuity; (v) the Mississippi River discontinuity; and (vi) the Apalachicola River and Mississippi River discontinuities. Although initially documented in animals, most of these patterns are also apparent in plants, providing support for phylogeographical generalizations. These patterns may generally be attributable to isolation and differentiation during Pleistocene glaciation, but in some cases may be older (Pliocene). Molecular studies sometimes agree with longstanding hypotheses of glacial refugia, but also suggest additional possible refugia, such as the southern Appalachian Mountains and areas close to the Laurentide Ice Sheet. Many species exhibit distinct patterns that reflect the unique, rather than the shared, aspects of species' phylogeographical histories. Furthermore, similar modern phylogeographical patterns can result from different underlying causal factors operating at different times (i.e. pseudocongruence). One underemphasized component of pseudocongruence may result from the efforts of researchers to categorize patterns visually - similar patterns may, in fact, not fully coincide, and inferring agreement may obscure the actual patterns and lead to erroneous conclusions. Our modelling analyses indicate no clear spatial patterning and support the hypothesis that phylogeographical structure in diverse temperate taxa is complex and was not shaped by just a few barriers.     

Comparative phylogeography of codistributed aquatic insects in western North America: insights into dispersal and regional patterns of genetic structure

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Refugia within refugia – patterns in endemism and genetic divergence are linked to Late Quaternary climate stability in the Iberian Peninsula

In Europe, southern peninsulas served as major refugia during Pleistocene cold periods. However, growing evidence has revealed complex patterns of glacial survival within these southern regions, with multiple glacial refugia within each larger refugial area. We investigated the extent to which patterns of endemism and phylogeographic are concordant across animal species in the Iberian Peninsula, one of the most important unglaciated areas in Europe during the Pleistocene, can be explained in terms of climatic stability. We found that historical climatic stability (notably climate velocity measures integrating macroclimatic shifts with local spatial topoclimate gradients) was often among the most important predictors of endemic species richness for different taxonomic groups using models that also incorporated measures of modern climate. Furthermore, for some taxonomic groups, climatic stability was also correlated with patterns of spatial concordance in interpopulation genetic divergence across multiple taxa, and private haplotypes were more frequently found in relatively stable areas. Overall, our results suggest that both endemism patterns and cross‐taxa concordant phylogeographic patterns across the Iberian Peninsula to some extent are linked to spatial variation in Late Quaternary climate stability, in agreement with the proposed ‘refugia‐within‐refugia’ scenario. © 2014 The Linnean Society of London, Biological Journal of the Linnean Society, 2014, 113 , 13–28.     

The roles of rivers and Pleistocene refugia in shaping genetic diversity in Praomys misonnei in tropical Africa

Aim This study aims to elucidate the phylogeography of the murid rodent Praomys misonnei and to document whether or not rain forest refugia and rivers structure patterns of diversity within this species. Location Tropical Africa, from Ghana to Kenya. Methods Patterns of genetic structure and signatures of population history (cytochrome b gene) were assessed in a survey of 229 individuals from 54 localities. Using maximum likelihood, Bayesian, network and genetic structure analyses, we inferred intra‐specific relationships and tested hypotheses for historical patterns of gene flow within P. misonnei. Results Our phylogenetic analyses reveal a strong phylogeographical structure. We identified four major geographical clades within P. misonnei: one clade in Ghana and Benin, a Nigerian clade, a West Central African clade and a Central and East African clade. Several subclades were identified within these four major clades. A signal of population expansion was detected in most clades or subclades. Coalescence within all of the major clades of P. misonnei occurred during the Middle Pleistocene and/or the beginning of Late Pleistocene. Main conclusions Our results suggest a role for both Pleistocene refugia and rivers in structuring genetic diversity in P. misonnei. This forest‐dwelling rodent may have been isolated in a number of forest fragments during arid periods and expanded its range during wetter periods. Potential forest refugia may have been localized in Benin–Ghana, south‐western Cameroon, southern Gabon, northern Gabon and eastern Democratic Republic of Congo–western Uganda. The Niger and/or the Cross Rivers, the Oubangui‐Congo, Sanaga, Ogooue and/or Ivindo Rivers probably stopped the re‐expansion of the species from relict areas.     

The influence of Pleistocene glacial refugia on tawny owl genetic diversity and phylogeography in western Europe

The glacial refugia hypothesis indicates that during the height of the Pleistocene glaciations the temperate species that are today widespread in western Europe must have survived in small and climatically favourable areas located in the southern peninsulas of Iberia, Italy and Balkans. One such species is the tawny owl, a relatively sedentary, nonmigratory bird presently distributed throughout Europe. It is a tree-nesting species closely associated with deciduous and mixed coniferous woodlands. In this study I used control region mtDNA sequences from 187 individuals distributed among 14 populations to determine whether current genetic patterns in tawny owl populations were consistent with postglacial expansion from peninsular refugia. European, North African and Asian tawny owls were found to represent three distinct lineages, where North Africa is the sister clade to all European owls. Within Europe, I found three well-supported clades that correspond to each of the three allopatric refugia. Expansion patterns indicate that owls from the Balkan refugium repopulated most of northern Europe, while expansion out of Iberia and Italy had only regional effects leading to admixture in France. Estimates of population divergence times between refugia populations are roughly similar, but one order of magnitude smaller between Greece and northern Europe. Based on a wide range of mutation rates and generation times, divergence between refugia appears to date to the Pleistocene.     

A phylogeographic, demographic and historical analysis of the short-tailed pit viper (Gloydius brevicaudus): evidence for early divergence and late expansion during the Pleistocene

The impact of quaternary glaciation in eastern China on local fanua and flora has been a topic of considerable interest. We used mitochondrial DNA (mtDNA) sequence data and coalescent simulations to test two general biogeographic hypothesis related to the effects of Pleistocene climatic fluctuations for a widespread ophidian species (Gloydius brevicaudus) in eastern China and Korean Peninsula. The phylogenetic analysis revealed three major lineages, the southeast Coastal, Yangtze and North Lineages. The latter two are closely related and jointly form a continental lineage. Divergence dating and coalescent simulations indicate a Late Pliocene to Early Pleistocene divergence between lineages from the southeast coast and continental interior, followed by a mid-to-late Pleistocene divergence between lineages from the north and the middle-lower Yangtze Valley across East China, suggesting that all these lineages predated the last glacial maximum. An overlapping range between the two lineages within the continental lineage and a secondary contact associated with ecological transition zones on the margins of the North China Plain were also observed. These results show that vicariance patterns dominated the history of G. brevicaudus. Though the climatic events of the Pleistocene have had a marked effect on the historical distribution and intra-specific divergence of reptiles in China, coalescent and non-coalescent demographic analyses indicate that all lineages of G. brevicaudus seem not to have been adversely affected by glacial cycles during the Late Pleistocene, presumably because of an increase in the amount of climatically mild habitat in East Asia due to a decline in elevation and the development of monsoons since the Mid-End Pleistocene.     

Historical climate modelling predicts patterns of current biodiversity in the Brazilian Atlantic forest

Aim We aim to propose validated, spatially explicit hypotheses for the late Quaternary distribution of the Brazilian Atlantic forest, and thereby provide a framework for integrating analyses of species and genetic diversity in the region. Location The Atlantic forest, stretching along the Brazilian coast. Methods We model the spatial range of the forest under three climatic scenarios (current climate, 6000 and 21,000 years ago) with BIOCLIM and MAXENT. Historically stable areas or refugia are identified as the set of grid cells for which forest presence is inferred in all models and time projections. To validate inferred refugia, we test whether our models are matched by the current distribution of the forest and by fossil pollen data. We then investigate whether the location of inferred forest refugia is consistent with current patterns of species endemism and existing phylogeographical data. Results Forest models agree with pollen records and predict a large area of historical forest stability in the central corridor (Bahia), as well as a smaller refuge (Pernambuco) along the Brazilian coast, matching current centres of endemism in multiple taxa and mtDNA diversity patterns in a subset of the species examined. Less historical stability is predicted in coastal areas south of the Doce river, which agrees with most phylogeographical studies in that region. Yet some widely distributed taxa show high endemism in the southern Atlantic forest. This may be due to limitations of the modelling approach, differences in ecology and dispersal capability, historical processes not contemplated by the current study or inadequacy of the available test data sets. Main conclusions Palaeoclimatic models predict the presence of historical forest refugia in the Atlantic rain forest and suggest spatial variation in persistence of forests through the Pleistocene, predicting patterns of biodiversity in several local taxa. The results point to the need for further studies to document genetic and species endemism in the relatively poorly known and highly impacted areas of Atlantic rain forests of north‐eastern Brazil.     

Population genetic isolation and limited connectivity in the purple finch (Haemorhous purpureus)

Using a combination of mitochondrial and z‐linked sequences, microsatellite data, and spatio‐geographic modeling, we examined historical and contemporary factors influencing the population genetic structure of the purple finch (Haemorhous purpureus). Mitochondrial DNA data show the presence of two distinct groups corresponding to the two subspecies, H. p. purpureus and H. p. californicus. The two subspecies likely survived in separate refugia during the last glacial maximum, one on the Pacific Coast and one east of the Rocky Mountains, and now remain distinct lineages with little evidence of gene flow between them. Southwestern British Columbia is a notable exception, as subspecies mixing between central British Columbia and Vancouver Island populations suggests a possible contact zone in this region. Z‐linked data support two mitochondrial groups; however, Coastal Oregon and central British Columbia sites show evidence of mixing. Contemporary population structure based on microsatellite data identified at least six genetic clusters: three H. p. purpureus clusters, two H. p. californicus clusters, and one mixed cluster, which likely resulted from high site fidelity and isolation by distance, combined with sexual selection on morphological characters reinforcing subspecies differences.     

Glacial refugia influence plant diversity patterns in the Mediterranean Basin

Aim The aims of this study were to assess the distribution of putative Mediterranean refugia of plants, to compare the locations of refugia and those of regional hotspots of plant biodiversity, and to provide a critical analysis of the Mediterranean refugium paradigm. Furthermore, we consider how biogeographical and genetic results can be combined to guide global conservation strategies. Location The Mediterranean region. Methods We started from a detailed analysis of the scientific literature (1993–2007) in order to identify refugia in the Mediterranean region, based on intra‐specific phylogeographical studies of plant species. We used population locations together with gene‐pool identity to establish the database, comparing patterns of phylogeographical concordance with the locations of Mediterranean refugia. We then tested the biogeographical congruence between two biodiversity components, namely phylogeographical refugia and regional hotspots. Results We identified 52 refugia in the Mediterranean bioclimatic region and confirmed the role played by the three major peninsulas, with a shared total of 25 refugia. We emphasize the importance of areas that have previously been attributed a lesser role (large Mediterranean islands, North Africa, Turkey, Catalonia). Of the 52 refugia identified, 33 are situated in the western Mediterranean Basin and 19 in the eastern part. The locations of the phylogeographically defined refugia are significantly associated with the 10 regional hotspots of plant biodiversity, with 26 of these refugia (i.e. 50%) occurring within the hotspots. Main conclusions The locations of refugia are determined by complex historical and environmental factors, the cumulative effects of which need to be considered because they have occurred since the Tertiary, rather than solely during the last glacial period. Refugia represent climatically stable areas and constitute a high conservation priority as key areas for the long‐term persistence of species and genetic diversity, especially given the threat posed by the extensive environmental change processes operating in the Mediterranean region. The refugia defined here represent ‘phylogeographical hotspots’; that is, significant reservoirs of unique genetic diversity favourable to the evolutionary processes of Mediterranean plant species.     

Pliocene and Pleistocene events shaping the genetic diversity within the central corridor of the Brazilian Atlantic Forest

Dinoponera lucida (Formicidae; Ponerinae) is an extinction‐threatened species of ant which is endemic in the central corridor of the Atlantic Forest. We used mitochondrial sequences of the Cox1, Cox2 and Cytb genes in order to infer some aspects of the evolutionary history and phylogeography of this ant. High genetic divergence and population structure were observed for the whole species. The current pattern of D. lucida diversity seems to be shaped during different geological times: middle Pliocene, early Pleistocene and mainly late Pleistocene, when the reduction of populations generated a structure pattern of the genetic variation of this species. Our data show that this structure results from the maintenance of populations of D. lucida within very small putative refuges to the south of the central Bahia refugium. We thus argue that, for some Atlantic forest endemic species, especially those resistant to very small fragments of forest, such as D. lucida, the small putative refuges were as important as, or even more important than, larger and stable refuges for the creation and maintenance of diversity, adding another piece to the puzzle of the mechanisms underlying local endemism. © 2010 The Linnean Society of London, Biological Journal of the Linnean Society, 2010, 101 , 949–960.     

Chloroplast DNA intraspecific phylogeography of plants from the Pacific Northwest of North America

Molecular studies of plants from the Pacific Northwest of North America suggest a recurrent pattern of genetic differentiation and geographic structuring. In each of five angiosperms and one fern species representing diverse life histories, cpDNA data indicate two clades of populations that are geographically structured. A northern group comprises populations from Alaska to central or southern Oregon, whereas populations from central Oregon southward to northern California form a southern group. In several of these species, a few populations having southern genotypes may have survived in glacial refugia further north in the Olympic Peninsula, Queen Charlotte Islands, and Prince of Wales Island. Allozyme data reveal a similar pattern of differentiation in several other plants from the Pacific Northwest. North-south partitioning of genotypes has also been reported for several animal species from this region. On a broader geographic scale, northsouth partitioning of genotypes has also been observed in other plants from western North America having a variety of geographic distributions. Some species also display a reduction of genetic variability in the northern portion of their range compared to the south. The data suggest strongly that past glaciation profoundly influenced the genetic architecture of the flora and fauna of the Pacific Northwest. Two alternative hypotheses are advanced to explain the geographic structuring of genotypes. First, past glaciation may have created discontinuities in the geographic distributions of plant species, with populations surviving in several well-isolated northern and southern refugia. Following glaciation, migration of genetically differentiated, once-isolated populations resulted in the formation of a continuous geographic distribution with a major genetic discontinuity. Alternatively, plants survived and subsequently migrated northward from a southern refugium, and a genotype became fixed in one or a few populations at the leading edge of recolonization. Subsequent long-distance dispersal from this leading edge resulted in a relatively uniform northern genotype that differs from the southern genotype(s). Whatever the underlying mechanism, Pleistocence glaciation may have molded the intraspecific genetic architecture of both plants and animals from the Pacific Northwest in a geographically similar manner. Future studies should seek to obtain a comprehensive phylogeography for regions that includes a diversity of both plants and animals.Dedicated to emer. Univ.-Prof. DrFriedrich Ehrendorfer on the occasion of his 70th birthday     

Phylogenomic approaches reveal how climate shapes patterns of genetic diversity in an African rain forest tree species

The world's second largest expanse of tropical rainforest is in Central Africa, and it harbours enormous species diversity. Population genetic studies have consistently revealed significant structure across Central African rainforest plants. In particular, previous studies have repeatedly demonstrated a north–south genetic discontinuity around the equatorial line, in a continuous expanse of rainforest where a climatic inversion is documented. Here, we took a phylogeographic approach by sequencing 351 nuclear markers in 112 individuals across the distribution of the African rainforest tree species Annickia affinis (Annonaceae). We showed for the first time that the north–south divide is the result of a single, major colonization event across the climatic inversion from an ancestral population located in Gabon. We suggested that differences in ecological niche of populations located on either side of this inversion may have contributed to this phylogenetic discontinuity. We found evidence for inland dispersal, predominantly in northern areas, and variable demographic histories among genetic clusters, indicating that populations responded differently to past climate change. We show how newly developed genomic tools can provide invaluable insights into our understanding of tropical rainforest evolutionary dynamics.     

Persistent genetic signatures of colonization in Brachionus manjavacas rotifers in the Iberian Peninsula

Recent phylogeographical assessments have consistently shown that continental zooplankton display high levels of population subdivision, despite the high dispersal capacity of their diapausing propagules. As such, there is an apparent paradox between observed cosmopolitanism in the zooplankton that is associated with long-distance dispersal, and strong phylogeographical structures at a regional scale. Such population dynamics, far from migration-drift equilibrium, have been shown in the rotifer species complex Brachionus plicatilis, a group of over a dozen species inhabiting salt lakes and coastal lagoons worldwide. Here we present the mitochondrial DNA phylogeography of one of these species, Brachionus manjavacas, in the Iberian Peninsula, where it often co-occurs with the morphologically similar species B. plicatilis sensu stricto. We obtained sequences from 233 individuals from diapausing eggs and clonal cultures from 16 lakes in the Iberian Peninsula, and a Tunisian lake. Two strongly supported deep mitochondrial DNA clades were found (A and B). Phylogenetic and nested clade analysis showed that clade A has a strong phylogeographical structure, with a strong similarity of phylogeographical patterns between B. manjavacas clade A and B. plicatilis s.s. These include (i) signatures of allopatric fragmentation between central and southern populations, and (ii) range expansions in the Iberian Peninsula, both likely to have occurred during the Pleistocene. We find evidence for a glacial refugium in the Guadiana basin. Clades A and B co-occurred in several of these lakes because of range expansion and secondary contact between both clades. The co-occurrence between B. plicatilis s.s. and B. manjavacas is not recent, and both species might have experienced similar environmental challenges during the Pleistocene. The strong correlation of genetic and geographical distance found suggests that historical events can lead to such correlation, mirroring the effects of 'isolation by distance' in equilibrium populations.     

Phylogeography of the Temminck’s Stint (Calidris temminckii): historical vicariance but little present genetic structure in a regionally endangered Palearctic wader

Aim We study the population differentiation and phylogeography of the Temminck’s Stint (Calidris temminckii). Specifically, we seek signs of past and present population size changes and dispersal events and evaluate management and conservation unit status of the populations. We also study the possibility of introgression as the origin of two mitochondrial DNA (mtDNA) lineages found and estimate the divergence time of the lineages. Location Northern Eurasia. Methods We analysed 583 bp of mtDNA control region domains I and II and 11 microsatellite loci from 13 localities throughout the breeding range. In addition, we used mitochondrial cytochrome c oxidase subunit I (COI), a barcoding gene, to search for signs of introgression. Results More population differentiation was found from microsatellites than from mtDNA, although differentiation was weak in both markers. Signs of past population growth were observed, in addition to more recent decline in some areas. Both control region and COI sequences revealed two maternal lineages coexisting in Fennoscandia and in north‐west Siberia. No signs of introgression were detected. Lineage divergence time was estimated to have occurred during the glacial periods of Pleistocene. Main conclusions Slight differences in mtDNA and microsatellite differentiation and diversity may reflect different features – such as the mutation rate and effective population size – of the markers used, or female‐biased dispersal pattern and high male site‐fidelity of the species. The coexistence of the two mitochondrial lineages is most likely a consequence of post‐glacial mixing of two refugial Pleistocene populations. Based on genetic information alone, global conservation concerns are not imminent. However, fast decline of a marginal Bothnian Bay population and the smallness and remoteness of a Central Yakutian population warrant conservation actions.     

The role of glacial cycles in promoting genetic diversity in the Neotropics: the case of cloud forests during the Last Glacial Maximum

The increasing aridity during the Last Glacial Maximum (LGM) has been proposed as a major factor affecting Neotropical species. The character and intensity of this change, however, remains the subject of ongoing debate. This review proposes an approach to test contrasting paleoecological hypotheses by way of their expected demographic and genetic effects on Neotropical cloud forest species. We reviewed 48 paleoecological records encompassing the LGM in the Neotropics. The records show contrasting evidence regarding the changes in precipitation during this period. Some regions remained fairly moist and others had a significantly reduced precipitation. Many paleoecological records within the same region show apparently conflicting evidence on precipitation and forest stability. From these data, we propose and outline two demographic/genetic scenarios for cloud forests species based on opposite precipitation regimes: the dry refugia and the moist forests hypotheses. We searched for studies dealing with the population genetic structure of cloud forest and other montane taxa and compared their results with the proposed models. To date, the few available molecular studies show insufficient genetic evidence on the predominance of glacial aridity in the Neotropics. In order to disentangle the climatic history of the Neotropics, the present study calls for a general multi‐disciplinary approach to conduct future phylogeographic studies. Given the contradictory paleoecological information, population genetic data on Neotropical cloud forest species should be used to explicitly test the genetic consequences of competing paleoecological models.     

The history of Seasonally Dry Tropical Forests in eastern South America: inferences from the genetic structure of the tree Astronium urundeuva (Anacardiaceae)

Today, the Seasonally Dry Tropical Forests (SDTF) of eastern South America occur as large, well-defined nuclei (e.g. Caatinga in the northeast) and as smaller enclaves within other vegetations (e.g. Cerrado and Chaco). In order to infer the way the present SDTF distribution was attained, the genetic structure of Astronium urundeuva, a tree confined to SDTF, was assessed using two chloroplast spacers and nine microsatellite loci. Five haplotypes were identified, whose distribution was spatially structured. The distribution of the two most common and divergent haplotypes suggested former vicariance and progressive divergence due to isolation. More recent range expansions of these two lineages subsequently occurred, leading to a secondary contact at the southern limit of the Caatinga SDTF nucleus. The multilocus-Bayesian approach using microsatellites consistently identified three groups of populations (Northeast, Central and Southwest). Isolation by distance was found in Northeast and Southwest groups whereas admixture was detected in the Central group, located at the transition between Caatinga and Cerrado domains. All together, the results support the existence of range expansions and secondary contact in the Central group. This study provides arguments that favour the existence of a previously more continuous formation of SDTF in eastern South America.