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Aim: The central and western Amazonia underwent several landscape changes during the Quaternary. Whereas the Riverine Barrier Hypothesis is traditionally used to explain the influence of rivers on speciation, processes such as river rearrangements have been overlooked to explain the geographic distribution and evolutionary history of Amazonia biota. Here, we tested how river rearrangements influenced the evolutionary history of uakari monkeys, genus Cacajao, a primate genus primarily associated with seasonally flooded forests in central and western Amazonia. Location: Central and Western Amazonia. Taxon: The genus Cacajao, including the black uakaris (C. melanocephalus, C. ayresi, C. hosomi); and the bald‐headed uakaris (C. calvus, C. amuna, C. rubicundus, C. ucayalii, C. novaesi). Methods: We performed a continuous phylogeographic analysis using 77 cytochrome b sequences to identify the origin and dispersal of Cacajao lineages. We used genome‐wide SNP variation (ddRADseq) to investigate population structure, gene flow and demographic history in Cacajao populations and used digital elevation models to identify landscape and riverscape characteristics that may have influenced the geographic distribution of Cacajao. Results: Our continuous phylogeographic reconstruction pointed out that the ancestral Cacajao lineage occupied the flooded forests of the Solimões River, in central Amazonia, at ~1.7 Mya and descendant lineages dispersed throughout central and western Amazonia more recently. We identified gene flow in both black and bald‐headed uakari populations, even across rivers considered barriers (e.g. the Negro River). Landscape analysis showed that river rearrangements influenced the geographic distribution and population structure in Cacajao. Historical demographic analyses suggest varied scenarios of population size changes among Cacajao monkeys consistent with periods of intense dynamism in flooded habitats and the formation of non‐flooded upland forests. Main Conclusion: Our results support that the river rearrangements have shaped the geographic distribution and divergence of recently diverged Cacajao lineages. Landscape and riverscape changes, along with retractions of the flooded forests, isolated some Cacajao populations in floodplain areas. Our study also suggests that these events led to the recent changes in demographic histories in species with a restricted geographic distribution. [ABSTRACT FROM AUTHOR]

Southern and northern glacial refugia are considered paradigms that explain the complex phylogeographical patterns and processes of European biota. Here, we provide a revisited statistical phylogeographical analysis of the pygmy shrew Sorex minutus Linnaeus, 1766 (Eulipotyphla, Soricidae), examining its genetic diversity, genetic differentiation and demographic history in the Mediterranean peninsulas and in Western and Central Europe. The results showed support for genetically distinct and diverse phylogeographical groups consistent with southern and northern glacial refugia, as expected from previous studies. We also identified geographical barriers concordant with glaciated mountain ranges during the Last Glacial Maximum (LGM), early diversification events dated between the Late Pleistocene and Early Holocene for the main phylogeographical groups, and recent (post-LGM) patterns of demographic expansions. This study is the most comprehensive investigation of this species to date, and the results have implications for the conservation of intraspecific diversity and the preservation of the evolutionary potential of S. minutus. [ABSTRACT FROM AUTHOR]

The wood mouse Apodemus sylvaticus is an opportunistic rodent that is found throughout most of the European mainland. It is present on many islands around the margins of the continent and in northern Africa. The species has been the subject of previous phylogeographical studies, although these have focussed on the more southerly part of its range. A substantial number of new samples, many of them from the periphery of the species' range, contribute to an exceptional dataset comprising 981 mitochondrial cytochrome b sequences. These new data provide sufficient resolution to transform our understanding of the survival of the species through the last glaciation and its subsequent re-colonization of the continent. The deepest genetic split that we found is in agreement with previous studies and runs from the Alps to central Ukraine, although we further distinguish two separate lineages in wood mice to the north and west of this line. It is likely that this part of Europe was colonized from two refugia, putatively located in the Iberian peninsula and the Dordogne or Carpathian region. The wood mouse therefore joins the growing number of species with extant populations that appear to have survived the Last Glacial Maximum in northern refugia, rather than solely in traditionally recognized refugial locations in the southern European peninsulas. Furthermore, the existence of a northern refugium for the species was predicted in a study of mitochondrial variation in a specific parasite of the wood mouse, demonstrating the potential value of data from parasites to phylogeographical studies. Lastly, the presence of related haplotypes in widely disparate locations, often on islands or separated by substantial bodies of water, demonstrates the propensity of the wood mouse for accidental human-mediated transport. [ABSTRACT FROM AUTHOR]

There is now considerable evidence for the survival of temperate species within glacial refugia that were situated at relatively high latitudes, notably the Carpathian Basin and Dordogne region in Europe. However, the prevalence of fossil remains in such locations is rarely matched by molecular evidence for their contribution to subsequent geographical and demographic expansion of the species in question. One obstacle to this has been insufficient analysis of modern samples from the relevant areas, in particular the parts of eastern Europe that surround the Carpathian refugium. In the present study, we examine the patterns of variation in mitochondrial DNA of the common vole ( Microtus arvalis), obtained from existing museum specimens and from newly-collected samples obtained in this area. We show that common voles from one of six extant mitochondrial DNA lineages have colonized most of the species' range in eastern Europe. We contend that the post-glacial dispersal of this lineage most likely originated from the Carpathian refugium, adding support to the argument that such northern refugia made an important contribution to existing genetic diversity in Europe. © 2015 The Linnean Society of London, Biological Journal of the Linnean Society, 2015, ●●, ●●-●●. [ABSTRACT FROM AUTHOR]

Overarching trends can be seen in European mammalian phylogeography, yet it is clear that species responded differently depending on adaptations to past environments. We built upon previous work on the phylogeography of weasels ( Mustela nivalis) in Europe by using well-preserved museum specimens from a proposed phylogeographic suture zone. The complete cytochrome b gene was amplified from 49 individuals from present-day Poland and analyzed with previously published data on a European scale to identify glacial refugia and infer recolonization processes. Bayesian coalescent analysis revealed the importance of the Last Glacial Maximum and the Younger Dryas in the diversification of, and demographic changes in, identified mitochondrial lineages. Our analysis, in conjunction with the available fossil data, strongly points to a Carpathian origin for one of the lineages, and further highlights the importance of this region as a refugium for European mammals. Mustela nivalis originating from this refugium appear to have a selective advantage over M. nivalis from other lineages in certain environments in the suture zone in central Europe, with climate clearly influencing the distribution of mitochondrial DNA lineages. This has important implications not only for our understanding of how past climatic events shaped the genetic architecture of species, but also how they will respond to current and future climatic changes. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, 106, 57-69. [ABSTRACT FROM AUTHOR]

[Display omitted] • We revised the taxonomic classification of bald-headed uakaris, genus Cacajao. • The use of a single mitochondrial marker did not recover the shallower relationships. • ddRADseq phylogenetic analyses retrieved five lineages of bald-headed uakaris. • We proposed a taxonomic arrangement with five species of bald-headed uakaris. • A new species is described based on molecular and morphological information. Bald uakaris, genus Cacajao , are Amazonian primates currently classified as one species and four subspecies based on the patterns of pelage coloration. In this study, we test if their current taxonomy is represented by the phylogenetic relationship of the main lineages retrieved from molecular data. We included, for the first time, all bald uakari taxa in a mitochondrial (cytochrome b) and genome-wide (ddRAD) phylogenetic analyses. We also examined the pattern of pelage colouration in specimens from zoological collections. Having determined the number of lineages using Maximum Likelihood and the species tree using coalescent analyses, we test their divergence time using a Bayesian approach. While the cytochrome b analysis only recovered two clades, the ddRAD analysis supported the reciprocal monophyly of five lineages of bald uakaris, with all clades including only individuals with distinct and exclusive diagnostic phenotypic characters. We found that species diversification in Cacajao occurred during the last 300 Kya and may have been influenced by the formation of rivers and flooded forests in western Amazonia. We propose that the four bald uakari subspecies currently recognised can be upgraded to species level and we describe the white uakaris from the basin of the Rio Tarauacá as a new species. [ABSTRACT FROM AUTHOR]