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Myotis riparius is an insectivorous bat species widely distributed in the Neotropics with evident geographical variation in morphological traits. We conducted an integrative study using mitochondrial DNA, qualitative and quantitative morphology, and current and past species distribution models to investigate the variation, population structure, and distributional limits within M. riparius populations. Phylogenetic inferences indicated that M. riparius is monophyletic, and populations are divided into geographically structured clades that split during the middle Pleistocene. There is no shared haplotype between geographical populations and strong evidence of partial restriction in gene flow. Morphological and morphometric variations revealed subtle distinctions among different populations, but little correspondence with molecular analysis. The distribution models indicated that M. riparius is associated with forest environments, with discontinuity between populations from South American ecoregions. Past distribution modelling, however, indicated that M. riparius had a larger distribution range in the Last Glacial Maximum than currently. Results of modelling and genetic analyses indicated that M. riparius consisted of a large, widespread, and panmictic (meta)population until the middle Pleistocene, when environmental changes driven by climatic dynamics fragmented and isolated the populations. Myotis riparius is here considered a complex of at least four allopatric and parapatric cryptic evolutionary units. [ABSTRACT FROM AUTHOR]

Los patrones biogeográficos de laflora mexicana, tanto en número de especies como de endemismos y relaciones entre áreas, han sido explicados a la luz de 3 teorías: 1) la dispersalista, donde México se considera receptor de elementos de diferentes fuentes o áreas geográficas, sobre todo si se toma en cuenta que está ubicado en la zona de transición entre la regiones neártica y neotropical que, junto con los autóctonos, han constituido un complejo mosaico de especies con diferentes orígenes, tanto espaciales como temporales; 2) la teoría de la vicarianza, que propone que hay una estrecha correspondencia entre la historia de la Tierra y la historia de la biota, por lo que el número de especies y su distribución tendrían que explicarse esencialmente de acuerdo con la compleja historia geológica de México y 3) el efecto de las glaciaciones pleistocénicas, que mediante eventos ecológicos e históricos explica los patrones contemporáneos de la distribución, con base en los cambios paleoclimáticos del pasado reciente. El debate fundamental al interior de la biogeografía histórica ha recaído en la importancia que tiene como fuente de evidencia para la taxonomía y viceversa. La biogeografía histórica, aunque posee una estrecha relación con la sistemática, es una disciplina independiente dentro de la biología comparada, que puede operar paralelamente a esta última. La biogeografía está en un proceso de revolución conceptual que ha propiciado la revisión de sus fundamentos y métodos. La utilización de diferentes métodos de una manera integrativa en un mismo análisis permite maximizar las bondades de cada uno de ellos.Biogeographical patterns of the Mexican flora are explained based on 3 different theories, considering number of species, endemisms, and relations among areas: 1) dispersalist theory, where Mexico has been considered as the receiver of elements of different sources or geographic areas, considering that it is located in the transition zone between the Nearctic and Neotropical regions, which along the autochthonous ones form a complex mixture of species with different origins, both spatial and temporal, 2) vicariant theory, that proposes a close relationship between the earth's history and the history of the biota, so that the number of species and their distribution may be explained by the complex geologic history of Mexico, and 3) pleistocenic glaciations, which explain the recent distributional patterns of plants based on ecological and historical arguments, based on paleoclimatic changes of the recent past. A continuous debate within historical biogeography has high lighted the importance of biogeography as source of evidence for taxonomy and vice versa. Historical biogeography has a close relationship with systematics, but is an independent discipline within comparative biology. Biogeography is undergoing a conceptual revolution that is causing a revision of its fundamentals and methods. The utilization of different methods in an integrative manner in the same analysis may maximize the advantages of each one.

Different diversification scenarios have been proposed to explain the origin of extant biodiversity. However, most existing meta-analyses of time-calibrated phylogenies rely on approaches that do not quantitatively test alternative diversification processes. Here, I highlight the shortcomings of using species divergence ranks, which is a method widely used in meta-analyses. Divergence ranks consist of categorizing cladogenetic events to certain periods of time, typically to either Pleistocene or to pre-Pleistocene ages. This approach has been claimed to shed light on the origin of most extant species and the timing and dynamics of diversification in any biogeographical region. However, interpretations drawn from such method often confound two fundamental questions in macroevolutionary studies, tempo (timing of evolutionary rate shifts) and mode ('how' and 'why' of speciation). By using simulated phylogenies under four diversification scenarios, constant-rate, diversity-dependence, high extinction, and high speciation rates in the Pleistocene, I showed that interpretations based on species divergence ranks might have been seriously misleading. Future meta-analyses of dated phylogenies need to be aware of the impacts of incomplete taxonomic sampling, tree topology, and divergence time uncertainties, as well as they might be benefited by including quantitative tests of alternative diversification models that acknowledge extinction and diversity dependence. [ABSTRACT FROM AUTHOR]

Hypochaeris leontodontoides is a rupicolous species endemic to the Atlas Mountains (Morocco), where it occurs in scattered populations. This study aims to understand the biogeographic structure of a high mountain species in a rather small area of NW Africa. We used Amplified Fragment Length Polymorphism (AFLP) to investigate the population structure and phylogeography of H. leontodontoides in 19 populations sampled from the entire species distribution range. Multivariate analyses including PCoA, UPGMA analysis, and Bayesian clustering were applied to infer the influence of past biogeographic events. The AFLP differentiation among the populations was high ( F = 0.508). A significant geographical pattern by mountain region was found. The different phylogeographical analyses revealed four main groups corresponding to four well-defined geographic regions: Middle Atlas, Eastern High Atlas, Central High Atlas, and Western High Atlas, and highlighted the Western High Atlas as the most divergent group. Our data also indicate two regions as refuges during the Pleistocene ice ages: the Middle Atlas and the northernmost area of the Western High Atlas. [ABSTRACT FROM AUTHOR]

A previous, geographically limited study, has found very little genetic structure in the water railRallus aquaticusbased on cytochrome oxidase I sequences. Adding samples from Romania, Montenegro, Germany and Spain, we investigated whether the new data confirm the picture of genetic homogeneity or if there is more diverse structure, e.g. due to survival in different Pleistocene refuges. Among 75 studied individuals, there were 12 haplotypes, one of them very common, the others differing in only one or two positions. The high haplotype diversity in Kazakhstan suggested that diversification has been ongoing for a longer time than in the other areas, assuming similar substitution rates across the entire species. Only one rare haplotype was shared between Kazakhstan and another region, specifically Romania. All other rare haplotypes had narrow distributions and probably evolved after the range expansion towards the west. Apparently, gene flow has been restricted in the recent past. The Romanian population was genetically intermediate between Kazakhstan and the western populations. The genetic structure of the populations supported a post-glacial out-of-Central-Asia scenario. [ABSTRACT FROM AUTHOR]

Aim Our aim was to document African rain forest tree diversity patterns to test whether they support one of the following hypotheses: the structure of tree species diversity is at equilibrium and mostly driven by neutral processes (H0); the structure of tree species diversity results from Pleistocene forest cover dynamics (H1); or the structure of tree species diversity results from ecological sorting along environmental gradients (H2). Location West Central Africa: the hilly region of Gabon, a putative Pleistocene forest refuge, and the adjacent flat littoral region, putatively colonized by forests from the hilly region after the last glaciation. Methods We used 103 standardized 0.1-ha tree plots distributed among five landscapes in the two regions. We partitioned the tree diversity within and among plots at a local and regional scale using the Hurlbert effective number of species framework. The explanatory power of geographical and elevational distances on species turnover was tested. At the landscape scale, we partitioned the beta diversity into nestedness and turnover components. Results Mean alpha and gamma diversities were much higher in the hilly region, where differences in elevation explained a significant part of species turnover. Substantial species turnover correlated with geographical distance also occurred in the littoral region despite its low elevational heterogeneity. Floristic turnover between plots from different regions remained stable whatever the elevational/geographical distances. At the regional scale, species replacement remained the main contributor to beta diversity (low nestedness values). Main conclusions The heterogeneous distribution of alpha and gamma diversity, similar levels of species turnover among plots and the low contribution of the nestedness component to beta diversity between hilly and littoral landscapes do not support hypotheses H0 and H1. The combined impacts of limited dispersal and ecological sorting along environmental gradients (H2) can explain patterns within regions. The marked floristic discontinuity between regions could reflect contrasting histories (two distinct refugia) although the role of contrasting environments cannot be discounted. [ABSTRACT FROM AUTHOR]

• Premise of the study: New insights into the history of the African rainforest can be gathered from the phylogeographic structures of their constituent species, but few studies have been performed in this ecosystem. We studied the phylogeographic structure of Santiria trimera, a primate- and bird-dispersed, dioecious tree typical of mature African rainforests. • Methods: We sequenced three chloroplast DNA (cpDNA) regions (trnL-F, rbeL, and rp136-infA-rps8) in 377 individuals from 42 populations. • Results: Sequence chromatograms regularly displayed double peaks of unequal heights. Cloning of PCR products and sequencing of outgroup taxa led to assigning the taller peak in ambiguous sequence positions to cpDNA. A total of 14 polymorphic cpDNA sites and 12 haplotypes were detected. Populations from three distinct biogeographic regions, namely, Upper Guinea, Lower Guinea, and the volcanic island of Silo Tom6, did not share any haplotype, indicating allopatric divergence, in Lower Guinea, Gabonese lbrests had high diversity mainly from the sympatry of two genetically divergent morphotypes, whereas forests of eastern Cameroon were less diversified. The two haplotypes of the morphotype without stilt roots were distributed north and south of the Ogooué River, suggesting refuges on both sides of the river bed. • Conclusions: The divergence between Upper and Lower Guinean rainforests is explained by the discontinuity of forest between those regions throughout most of the Quaternary. The distribution of rare endemic haplotypes concurred with proposed Pleistocene rainforest refuges in west and southwest Cameroon. Overall, phylogeographic structure is consistent with the biogeographic hypotheses largely based on patterns of species diversity. [ABSTRACT FROM AUTHOR]

Abstract: Nucleotide sequence data from a mitochondrial gene (16S) and two nuclear genes (c-mos, RAG-1) were used to evaluate the monophyly of the genus Coleodactylus, to provide the first phylogenetic hypothesis of relationships among its species in a cladistic framework, and to estimate the relative timing of species divergences. Maximum Parsimony, Maximum Likelihood and Bayesian analyses of the combined data sets retrieved Coleodactylus as a monophyletic genus, although weakly supported. Species were recovered as two genetically and morphological distinct clades, with C. amazonicus populations forming the sister taxon to the meridionalis group (C. brachystoma, C. meridionalis, C. natalensis, and C. septentrionalis). Within this group, C. septentrionalis was placed as the sister taxon to a clade comprising the rest of the species, C. meridionalis was recovered as the sister species to C. brachystoma, and C. natalensis was found nested within C. meridionalis. Divergence time estimates based on penalized likelihood and Bayesian dating methods do not support the previous hypothesis based on the Quaternary rain forest fragmentation model proposed to explain the diversification of the genus. The basal cladogenic event between major lineages of Coleodactylus was estimated to have occurred in the late Cretaceous (72.6±1.77Mya), approximately at the same point in time than the other genera of Sphaerodactylinae diverged from each other. Within the meridionalis group, the split between C. septentrionalis and C. brachystoma + C. meridionalis was placed in the Eocene (46.4±4.22Mya), and the divergence between C. brachystoma and C. meridionalis was estimated to have occurred in the Oligocene (29.3±4.33Mya). Most intraspecific cladogenesis occurred through Miocene to Pliocene, and only for two conspecific samples and for C. natalensis could a Quaternary differentiation be assumed (1.9±1.3Mya). [Copyright &y& Elsevier]

Like many fishes on coral reefs, the false clown anemonefish, Amphiprion ocellaris, has a life history with two different phases: adults are strongly site attached, whereas larvae are planktonic. Therefore, the larvae have the potential to disperse, but the degree of dispersal potential depends primarily on the period of the larval stage, which is only 8–12 days in A. ocellaris. In this study, we investigated the genetic population structure and gene flow in A. ocellaris across the Indo-Malay Archipelago by analysing a fragment of the mitochondrial control region. Population genetic analysis, usingamova, revealed a significant and high overall ΦST-value of 0.241 ( P<0.001), clearly showing limited gene flow. Haplotype network analysis detected eight distinct clades corresponding mainly to different geographical areas, which were most probably separated during sea level low stands in the Pleistocene. The distribution of the clades among the different populations indicated slow partial re-mixing mainly in the central region of the archipelago. Major surface currents seem to facilitate larval dispersal, indicated by higher connectivity along major surface currents in the region (e.g. Indonesian Throughflow). Four main groups were found by the hierarchicalamova within the archipelago. These different genetic lineages should be managed and protected as separate ornamental fishery stocks and resource contributing to the genetic diversity of the area. Regarding the high diversity and the differentiation among areas within the Indo-Malay Archipelago of A. ocellaris populations, the centre-of-origin theory is supported to be the main mechanism by which the high biodiversity evolved in this area. [ABSTRACT FROM AUTHOR]

Abstract: The Ceroxyloideae is a small but heterogeneous subfamily of palms (Arecaceae, Palmae). It includes a Caribbean lineage (tribe Cyclospathae), a southern hemisphere disjunction (tribe Ceroxyleae), and an amphi-Andean element (tribe Phytelepheae), until recently considered a distinct subfamily (Phytelephantoideae) due to its highly derived morphology. A variety of hypotheses have been proposed to account for the biogeography of the subfamily, involving Gondwanan vicariance, austral interplate dispersal from South America to Australia via Antarctica, Andean orogeny, and Pleistocene refuges. We assessed the systematic classification and biogeography of the group based on a densely sampled phylogeny using >5.5kb of DNA sequences from three plastid and two nuclear genomic regions. The subfamily and each of its three tribes were resolved as monophyletic with high support. Divergence time estimates based on penalized likelihood and Bayesian dating methods indicate that Gondwanan vicariance is highly unlikely as an explanation for basic disjunctions in tribe Ceroxyleae. Alternative explanations include a mid-Tertiary trans-Atlantic/trans-African dispersal track and the “lemurian stepping stones” hypothesis. Austral interplate dispersal of Oraniopsis to Australia could have occurred, but apparently only in the mid-Eocene/early Oligocene interval after global cooling had begun. Our data do not support Pleistocene climatic changes as drivers for speciation in the Andean-centered Phytelepheae as previously proposed. Radiation in this tribe coincides largely with the major uplift of the Andes, favoring Andean orogeny over Pleistocene climatic changes as a possible speciation-promoting factor in this tribe. [Copyright &y& Elsevier]

TheLycaeidesbutterfly species complex in North America consists of two nominal, morphologically defined species. These butterflies are ecologically diverse and appear to be distributed as a geographically complex mosaic of locally differentiated populations that may be undergoing adaptive radiation. We asked whether patterns of molecular genetic variation within the species complex are congruent with currently recognized morphological species and whether the distribution of molecular variation is consistent with the hypothesis that Pleistocene climate changes contributed to the process of differentiation within the genus. Variation in the form of the genitalia from 726 males from 59 populations clearly distinguishes both species with only six populations containing morphologically intermediate or ambiguous individuals. However, partitioning of molecular variance in a 236 bp section of the mitochondrial AT-rich region from 628 individuals (57 populations) surveyed using single strand conformation polymorphism analysis (SSCP) indicates that only 26% of the total genetic variation is distributed along nominal species boundaries as defined by morphology. Instead, three phylogeographical groups were detected, represented by three major haplotype clades, which account for 90% of the total genetic variance. Pleistocene glaciations appear to have fostered divergence during glacial maxima, while postglacial range expansions created opportunities for gene exchange and reticulation along suture zones between geographical groups. Data presented here allow us to make inferences about the history of the species complex. However, evidence of ancestral polymorphism and reticulation limit our ability to define species boundaries based on mitochondrial DNA sequence variation. [ABSTRACT FROM AUTHOR]

Attempts by biogeographers to understand biotic diversification in the Amazon have often employed contemporary species distribution patterns to support particular theories, such as Pleistocene rainforest refugia, rather than to test among alternative hypotheses. Suture zones, narrow regions where multiple contact zones and hybrid zones between taxa cluster, have been seen as evidence for past expansion of whole biotas that have undergone allopatric divergence in vicariant refuges. We used coalescent analysis of mutilocus sequence data to examine population split times in 22 pairs of geminate taxa in ithomiine and heliconiine butterflies. We test a hypothesis of simultaneous divergence across a suture zone in NE Peru. Our results reveal a scattered time course of diversification in this suture zone, rather than a tight cluster of split times. Additionally, we find rapid diversification within some lineages such as Melinaea contrasting with older divergence within lineages such as the Oleriina (Hyposcada and Oleria). These results strongly reject simple vicariance as a cause of the suture zone. At the same time, observed lineage effects are incompatible with a series of geographically coincident vicariant events which should affect all lineages similarly. Our results suggest that Pleistocene climatic forcing cannot readily explain this Peruvian suture zone. Lineage-specific biological traits, such as characteristic distances of gene flow or varying rates of parapatric divergence, may be of greater importance., (© 2010 Blackwell Publishing Ltd.)