Recent years have witnessed a proliferation of quantitative methods for biogeographic inference. In particular, novel parametric approaches represent exciting new opportunities for the study of range evolution. Here, ...Recent years have witnessed a proliferation of quantitative methods for biogeographic inference. In particular, novel parametric approaches represent exciting new opportunities for the study of range evolution. Here, we review a selection of current methods for biogeographic analysis and discuss their respective properties. These methods include generalized parsimony approaches, weighted ancestral area analysis, dispersal-vicariance analysis, the dispersal--extinction--cladogenesis model and other maximum likelihood approaches, and Bayesian stochastic mapping of ancestral ranges, including a novel approach to inferring range evolution in the context of island biogeography. Some of these methods were developed specifically for problems of ancestral range reconstruction, whereas others were designed for more general problems of character state reconstruction and subsequently applied to the study of ancestral ranges. Methods for reconstructing ancestral history on a phylogenetic tree differ not only in the types of ancestral range states that are allowed, but also in the various historical events that may change the ancestral ranges. We explore how the form of allowed ancestral ranges and allowed transitions can both affect the outcome of ancestral range estimation. Finally, we mention some promising avenues for future work in the development of model-based approaches to biogeographic analysis.展开更多
This is the opening paper in the special issue of Fungal Diversity,which collates the data on defining species.Defining and recognizing species has long been a controversial issue.Since Darwin’s proposed origin of sp...This is the opening paper in the special issue of Fungal Diversity,which collates the data on defining species.Defining and recognizing species has long been a controversial issue.Since Darwin’s proposed origin of species,over 30 species criteria have been brought forth and used to define species boundaries.In recent times,phylogenetic analyses based on multiple loci have been extensively used as a method to define species boundaries.However,only a few mycologists are aware that phylogenetic species criteria can mask discordances among fungal groups,leading to inaccurately defined species bounda-ries.In the current review,we discuss species recognition criteria,how and where these criteria can be applied along with their limitations and derived alternatives.In order to delimit fungal species,authors need to take into account not only the phylogenetic and phenotypic coherence,but also the timing of events that lead to fungal speciation and subsequent diversi-fications.Variations in the rate of phenotypic diversifications and convergent fungal evolution make it difficult to establish a universal species recognition criterion.The best practice can only be defined in the context of each fungal group.In this review,we provide a set of guidelines,encouraging an integrative taxonomic approach for species delimitation that can be used to define fungal species boundaries in the future.The other papers in this special issue deal with fungal speciation in Ascomycota,Dothideomycetes,Basidiomycota,basal fungi,lichen-forming fungi,plant pathogenic fungi,and yeasts.展开更多
We tested the role of interspecific competition in driving species distribution at multiple spatial scales using two sibl- ing species of Galerida larks （G cristata and G. theklae） in Morocco （sympatry）, Balearic ...We tested the role of interspecific competition in driving species distribution at multiple spatial scales using two sibl- ing species of Galerida larks （G cristata and G. theklae） in Morocco （sympatry）, Balearic islands （G theklae only） and Israel （G cristata only）. We first investigated regional-scale determinants by contrasting allopatric versus sympatric patterns in five distinct habitat types. We next focused on a single habitat used by both species, the coastal sand dunes. Dune quadrats were established along the Moroccan coast and completed by a quadrat in the nearest distinct landscape habitat. Poisson regressions were used to model Galerida counts together with ecological predictors as concerns the climate, topography, vegetation structure and soil gra- nulometry. At the local scale, both species preferred grey dunes over white sand dunes, and both were negatively affected by the abundance of the congeneric species in the dune. However, we found that G theklae tended to replace G. cristata in more arid sand dunes, even if the transition was not strictly clinal. Instead, the transition occurred when the surrounding landscape changed from coastal wetlands to bathas （grasslands with shrubs）, highlighting the importance of habitat composition at the landscape scale. The fact that G cristata used bathas in allopatry, but not in sympatry, suggested that the competitive environment contri- buted to determine sand dune occupancy. We suggest that landscape-level effects may be pivotal in explaining species distribu- tion not only at the local scale, by affecting the pool of potential immigrants, but also at the regional scale, by contributing to species＇ range limit [Current Zoology 61 （1）： 10-22, 2015].展开更多
基金support from the National Institute of Environmental Health Sciences (USA) training grant to the NCSU Bioinformatics Research Centersupported by National Institutes of Health (USA) grant no.GM070806
文摘Recent years have witnessed a proliferation of quantitative methods for biogeographic inference. In particular, novel parametric approaches represent exciting new opportunities for the study of range evolution. Here, we review a selection of current methods for biogeographic analysis and discuss their respective properties. These methods include generalized parsimony approaches, weighted ancestral area analysis, dispersal-vicariance analysis, the dispersal--extinction--cladogenesis model and other maximum likelihood approaches, and Bayesian stochastic mapping of ancestral ranges, including a novel approach to inferring range evolution in the context of island biogeography. Some of these methods were developed specifically for problems of ancestral range reconstruction, whereas others were designed for more general problems of character state reconstruction and subsequently applied to the study of ancestral ranges. Methods for reconstructing ancestral history on a phylogenetic tree differ not only in the types of ancestral range states that are allowed, but also in the various historical events that may change the ancestral ranges. We explore how the form of allowed ancestral ranges and allowed transitions can both affect the outcome of ancestral range estimation. Finally, we mention some promising avenues for future work in the development of model-based approaches to biogeographic analysis.
基金Authors would like to thank the Thailand Research Fund entitled“Impact of climate change on fungal diversity and biogeography in the Greater Mekong Sub region”(grant number RDG6130001).
文摘This is the opening paper in the special issue of Fungal Diversity,which collates the data on defining species.Defining and recognizing species has long been a controversial issue.Since Darwin’s proposed origin of species,over 30 species criteria have been brought forth and used to define species boundaries.In recent times,phylogenetic analyses based on multiple loci have been extensively used as a method to define species boundaries.However,only a few mycologists are aware that phylogenetic species criteria can mask discordances among fungal groups,leading to inaccurately defined species bounda-ries.In the current review,we discuss species recognition criteria,how and where these criteria can be applied along with their limitations and derived alternatives.In order to delimit fungal species,authors need to take into account not only the phylogenetic and phenotypic coherence,but also the timing of events that lead to fungal speciation and subsequent diversi-fications.Variations in the rate of phenotypic diversifications and convergent fungal evolution make it difficult to establish a universal species recognition criterion.The best practice can only be defined in the context of each fungal group.In this review,we provide a set of guidelines,encouraging an integrative taxonomic approach for species delimitation that can be used to define fungal species boundaries in the future.The other papers in this special issue deal with fungal speciation in Ascomycota,Dothideomycetes,Basidiomycota,basal fungi,lichen-forming fungi,plant pathogenic fungi,and yeasts.
文摘We tested the role of interspecific competition in driving species distribution at multiple spatial scales using two sibl- ing species of Galerida larks （G cristata and G. theklae） in Morocco （sympatry）, Balearic islands （G theklae only） and Israel （G cristata only）. We first investigated regional-scale determinants by contrasting allopatric versus sympatric patterns in five distinct habitat types. We next focused on a single habitat used by both species, the coastal sand dunes. Dune quadrats were established along the Moroccan coast and completed by a quadrat in the nearest distinct landscape habitat. Poisson regressions were used to model Galerida counts together with ecological predictors as concerns the climate, topography, vegetation structure and soil gra- nulometry. At the local scale, both species preferred grey dunes over white sand dunes, and both were negatively affected by the abundance of the congeneric species in the dune. However, we found that G theklae tended to replace G. cristata in more arid sand dunes, even if the transition was not strictly clinal. Instead, the transition occurred when the surrounding landscape changed from coastal wetlands to bathas （grasslands with shrubs）, highlighting the importance of habitat composition at the landscape scale. The fact that G cristata used bathas in allopatry, but not in sympatry, suggested that the competitive environment contri- buted to determine sand dune occupancy. We suggest that landscape-level effects may be pivotal in explaining species distribu- tion not only at the local scale, by affecting the pool of potential immigrants, but also at the regional scale, by contributing to species＇ range limit [Current Zoology 61 （1）： 10-22, 2015].
