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
Based on the variation of site 34, 46, 241, 305 and 322 in the 18S-ITS1 rDNA sequence, 19 Carchesium polypinum populations collected from eight provinces of China were separated into northern and southern population a...Based on the variation of site 34, 46, 241, 305 and 322 in the 18S-ITS1 rDNA sequence, 19 Carchesium polypinum populations collected from eight provinces of China were separated into northern and southern population along the delineation between the Yangtze River and the Pearl River. This geographic distribution pattern of Carchesium polypinum maybe results from two factors: the vicariance resulting from the formation of the delineation between the Pearl River and the Yangtze River accompanied with the uplift of Qinghai-Xizang Plateau, and the different dispersal paths of C. polypinum affected by the climate.展开更多
Nothofagus is regarded as a key group for interpreting Southern Pacific biogeographical history.Based on a molecular phylogenetic tree,a quantitative dispersal-vicariance analysis(DIVA) of the genus is presented.The r...Nothofagus is regarded as a key group for interpreting Southern Pacific biogeographical history.Based on a molecular phylogenetic tree,a quantitative dispersal-vicariance analysis(DIVA) of the genus is presented.The results indicate that the ancestral area of Nothofagus is a broad realm almost including the total extant distribution pattern of the genus rather than a so-named center of origin.Integrated with the paleogeography,the time of origin and subsequent diversification is inferred to have started in the Late Cretaceous.Most vicariance and dispersal events should be contained in that period.Vicariance events versus dispersal events play a dominant rule in speciation.The dispersal events are hypothesized to happen from the Late Cretaceous to Eocene in terms of the geological history.Rich fossils are collected in the Eocene.South America,comprising three subgenera of Nothofagus,should be considered as a diversification region,in which the distribution of the species of subgenus Fuscospora and subgenus Nothofagus are explained by dispersal events during the Late Cretaceous-Late Eocene.展开更多
The genus Caragana Fabr., consisting of approximately 70 species, has a temperate Asian distribution and occurs mainly in the drought and cold regions of the northwestern and southwestern Tibetan Plateau of China. The...The genus Caragana Fabr., consisting of approximately 70 species, has a temperate Asian distribution and occurs mainly in the drought and cold regions of the northwestern and southwestern Tibetan Plateau of China. The distribution pattern of the genus was investigated using dispersal-vicariance analysis （DIVA）, The results indicate that vicariance versus dispersal plays a major role in the evolution of the genus and that short-distance dispersal also exists. There is no fossil record of this genus. Therefore, Caragana is inferred as an advanced taxon in terms of its limited temperate Asian distribution. Based on the morphological variation and ecological adaptation in Caragana, the generic speciation is postulated to be related to the uplifting of the Tibetan Plateau and to the increasing arid conditions of Central Asian lands since the Neogene. The Mongolian Plateau and the Tibetan Plateau are hypothesized as the barriers of vicariance between East Asia and western Central Asia.展开更多
Caryopteris incana is a continental plant, transferred to Japan from continental Asia via a land bridge between the Korean Peninsula and Tsushima Islands during a glacial period. It currently grows wild in West Kyushu...Caryopteris incana is a continental plant, transferred to Japan from continental Asia via a land bridge between the Korean Peninsula and Tsushima Islands during a glacial period. It currently grows wild in West Kyushu, Japan. In a previous study, we investigated the distribution of C. incana in the Tsushima Islands and confirmed the genetic structure of populations by using chloroplast DNA sequence analysis, suggesting that different haplotypes were distributed in the same area. Thus, it seemed that populations of C. incana throughout the Tsushima Islands colonized at different times;each haplotype had remained within its population without mixing. In this study, we conducted fieldwork to construct a detailed distribution map in West Kyushu excluding the Tsushima Islands. Additionally, we confirmed genetic structure of the C. incana population in these areas by using chloroplast DNA sequence analysis to study the intraspecific phylogenetic relationship of C. incana in Japan. We confirmed 37 natural populations in 257 locations throughout West Kyushu excluding the 72 natural populations in the Tsushima Islands. We also confirmed a recent decreasing trend in the number of natural populations in the Nagasaki Mainland. Using the leaves of individuals cultivated from seeds collected from each natural population, we analyzed the chloroplast DNA sequence variations. Among the investigated populations, sequence variations were confirmed in six regions of chloroplast DNA, and those haplotypes were mainly classified into two groups distributed in different areas on the phylogenetic tree. This finding revealed that the common ancestor of C. incana in Japan diverged early into two groups, followed by a fragmentation in population distribution for each area. The haplotype network almost reflected the geographical distribution on haplotypes. However, several haplotypes that were distributed in other areas were confirmed in the Nagasaki Mainland, suggesting a complicated distribution formation in the past.展开更多
The historical relationships of nine areas of endemism of the tropical montane cloud forests(TMCFs)were analysed based on a temporal cladistic biogeographical approach.Three cladistic biogeographical analyses were con...The historical relationships of nine areas of endemism of the tropical montane cloud forests(TMCFs)were analysed based on a temporal cladistic biogeographical approach.Three cladistic biogeographical analyses were conducted based on 29cladograms of terrestrial taxa by partitioning them into three time-slices,namely,Miocene,Pliocene,and Pleistocene.The results showed different area relationships over time.For the Miocene and Pliocene time slices,the Isthmus of Tehuantepec acted as a geographic barrier that fragmented the TMCFs into two portions:west of the Isthmus and east of the Isthmus.In the case of the Pleistocene,the TMCFs were broken into two portions,one related to the Neotropical region and the other to the Nearctic region.Furthermore,the analyses allowed us to detect the influences of different geological and paleoclimatological events on the distribution of the TMCFs over time.Therefore,the TMCFs current distribution might have been driven by geological events during the Miocene-Pliocene,whereas climatic fluctuations have the highest impact during the Pleistocene.展开更多
The relationships of Madagascan plant and animal taxa have been the object of much fascination, Madagascar sharing numerous lineages with Africa, others with Asia, Australia, or the Americas, and many others being of ...The relationships of Madagascan plant and animal taxa have been the object of much fascination, Madagascar sharing numerous lineages with Africa, others with Asia, Australia, or the Americas, and many others being of uncertain relationships. In commonly accepted global regionalization schemata, Madagascar is treated together with Africa for animals, and with Africa, tropical Asia and the Pacific islands in the case of plants. Here we examine the similarities between the biotic assemblages of （i） tropical Africa, （ii） Madagascar, and （iii） the rest of the world, on a basic taxonomic level, considering the families of vascular plants and vertebrates as analysis units. The percentages of endemic families, families shared pair-wise between regions, or pre- sent in all three, are roughly similar between the two broad groups, though plant families with ranges limited to one region are proportionally fewer. In dendrograms and multidimensional scaling plots for different groups, Madagascar clusters together with Africa, Asia or both, and sometimes with smaller Indian Ocean Islands, but quite often （though not in plants） as a convincingly separate cluster. Our results for vertebrates justify the status of full zoogeographic region for Madagascar, though an equally high rank in geobotanical regionalization would mean also treating Africa and Tropical Asia as separate units, which would be debata- ble given the overall greater uniformity of plant assemblages. Beyond the Madagascan focus of this paper, the differences be- tween plant and vertebrate clusters shown here suggest different levels of ecological plasticity at the same taxonomic level, with plant families being much more environmentally-bound, and thus clustering along biome lines rather than regional lines [Current Zoology 58 （3）： 363-374, 2012].展开更多
Based on a cladistic biogeographic analysis of 6 species-level phylogenies of harvestman taxa, wesearched for congruence in the historical relationships of 12 areas of endemism of the BrazilianAtlantic Rain Forest. We...Based on a cladistic biogeographic analysis of 6 species-level phylogenies of harvestman taxa, wesearched for congruence in the historical relationships of 12 areas of endemism of the BrazilianAtlantic Rain Forest. We constructed general area cladograms using Primary Brooks ParsimonyAnaJysis （BPA）, BPA of nodes, and paralogy-free subtree analysis. These analyses resulted in 6general area cladograms, that allow to infer a general pattern of the relationships among areas ofendemism from the Brazilian Atlantic Rain Forest. Northern areas resulted related basally showingmain disjunctions at the Doce River Valley and Todos os Santos Bay/S^o Francisco River Valley.The remaining areas of endemism were included in a southern and a southeastern block, sepa-rated by the Ribeira do Iguape Valley. Incongruence Length Differences tests showed no significantincongruence among the resulting cladograms and other matrix partitions. We concluded that tec-tonism and ancient marine transgressions were the probable processes responsible for the maindisjunctions, whereas Neogene refugia seem to have caused the more recent disjunctions. Thegeneral pattern and redundancy in area relationships suggest a model of main reiterative barriersin diversification at multiple times for the evolution of the Atlantic Rain Forest. The renewal of cla-distic biogeography and the search for common biogeographic patterns are discussed.展开更多
Molecular dating techniques require the use of calibrations, which are usually fossil or geological vicariance-based. Fossil calibrations have been criticised because they result only in minimum age estimates. Based o...Molecular dating techniques require the use of calibrations, which are usually fossil or geological vicariance-based. Fossil calibrations have been criticised because they result only in minimum age estimates. Based on a historical biogeographic perspective, I suggest that vicariance-based calibrations are more dangerous. Almost all analytical methods in historical biogeog- raphy are strongly biased towards inferring vicariance, hence vicariance identified through such methods is unreliable. Other studies, especially of groups found on Gondwanan fragments, have simply assumed vicariance. Although it was previously be- lieved that vicariance was the predominant mode of speciation, mounting evidence now indicates that speciation by dispersal is common, dominating vicaziance in several groups. Moreover, the possibility of speciation having occurred before the said geo- logical event cannot be precluded. Thus, geological calibrations can under- or overestimate times, whereas fossil calibrations al- ways result in minimum estimates. Another major drawback of vicariant calibrations is the problem of circular reasoning when the resulting estimates are used to infer ages of biogeographic events. I argue that fossil-based dating is a superior alternative to vicariance, primarily because the strongest assumption in the latter, that speciation was caused by the said geological process, is more often than not the most tenuous. When authors prefer to use a combination of fossil and vicariant calibrations, one suggestion is to report results both with and without inclusion of the geological constraints. Relying solely on vicariant calibrations should be strictly avoided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.
文摘Based on the variation of site 34, 46, 241, 305 and 322 in the 18S-ITS1 rDNA sequence, 19 Carchesium polypinum populations collected from eight provinces of China were separated into northern and southern population along the delineation between the Yangtze River and the Pearl River. This geographic distribution pattern of Carchesium polypinum maybe results from two factors: the vicariance resulting from the formation of the delineation between the Pearl River and the Yangtze River accompanied with the uplift of Qinghai-Xizang Plateau, and the different dispersal paths of C. polypinum affected by the climate.
基金supported by Important Direction for Knowledge Innovation Project,CAS (KZCX2-EW-305)Xinjiang Institute of Ecology and Geography,CAS
文摘Nothofagus is regarded as a key group for interpreting Southern Pacific biogeographical history.Based on a molecular phylogenetic tree,a quantitative dispersal-vicariance analysis(DIVA) of the genus is presented.The results indicate that the ancestral area of Nothofagus is a broad realm almost including the total extant distribution pattern of the genus rather than a so-named center of origin.Integrated with the paleogeography,the time of origin and subsequent diversification is inferred to have started in the Late Cretaceous.Most vicariance and dispersal events should be contained in that period.Vicariance events versus dispersal events play a dominant rule in speciation.The dispersal events are hypothesized to happen from the Late Cretaceous to Eocene in terms of the geological history.Rich fossils are collected in the Eocene.South America,comprising three subgenera of Nothofagus,should be considered as a diversification region,in which the distribution of the species of subgenus Fuscospora and subgenus Nothofagus are explained by dispersal events during the Late Cretaceous-Late Eocene.
文摘The genus Caragana Fabr., consisting of approximately 70 species, has a temperate Asian distribution and occurs mainly in the drought and cold regions of the northwestern and southwestern Tibetan Plateau of China. The distribution pattern of the genus was investigated using dispersal-vicariance analysis （DIVA）, The results indicate that vicariance versus dispersal plays a major role in the evolution of the genus and that short-distance dispersal also exists. There is no fossil record of this genus. Therefore, Caragana is inferred as an advanced taxon in terms of its limited temperate Asian distribution. Based on the morphological variation and ecological adaptation in Caragana, the generic speciation is postulated to be related to the uplifting of the Tibetan Plateau and to the increasing arid conditions of Central Asian lands since the Neogene. The Mongolian Plateau and the Tibetan Plateau are hypothesized as the barriers of vicariance between East Asia and western Central Asia.
文摘Caryopteris incana is a continental plant, transferred to Japan from continental Asia via a land bridge between the Korean Peninsula and Tsushima Islands during a glacial period. It currently grows wild in West Kyushu, Japan. In a previous study, we investigated the distribution of C. incana in the Tsushima Islands and confirmed the genetic structure of populations by using chloroplast DNA sequence analysis, suggesting that different haplotypes were distributed in the same area. Thus, it seemed that populations of C. incana throughout the Tsushima Islands colonized at different times;each haplotype had remained within its population without mixing. In this study, we conducted fieldwork to construct a detailed distribution map in West Kyushu excluding the Tsushima Islands. Additionally, we confirmed genetic structure of the C. incana population in these areas by using chloroplast DNA sequence analysis to study the intraspecific phylogenetic relationship of C. incana in Japan. We confirmed 37 natural populations in 257 locations throughout West Kyushu excluding the 72 natural populations in the Tsushima Islands. We also confirmed a recent decreasing trend in the number of natural populations in the Nagasaki Mainland. Using the leaves of individuals cultivated from seeds collected from each natural population, we analyzed the chloroplast DNA sequence variations. Among the investigated populations, sequence variations were confirmed in six regions of chloroplast DNA, and those haplotypes were mainly classified into two groups distributed in different areas on the phylogenetic tree. This finding revealed that the common ancestor of C. incana in Japan diverged early into two groups, followed by a fragmentation in population distribution for each area. The haplotype network almost reflected the geographical distribution on haplotypes. However, several haplotypes that were distributed in other areas were confirmed in the Nagasaki Mainland, suggesting a complicated distribution formation in the past.
基金the CONACyT 478077partially financed by DGAPA-PAPIIT 220621。
文摘The historical relationships of nine areas of endemism of the tropical montane cloud forests(TMCFs)were analysed based on a temporal cladistic biogeographical approach.Three cladistic biogeographical analyses were conducted based on 29cladograms of terrestrial taxa by partitioning them into three time-slices,namely,Miocene,Pliocene,and Pleistocene.The results showed different area relationships over time.For the Miocene and Pliocene time slices,the Isthmus of Tehuantepec acted as a geographic barrier that fragmented the TMCFs into two portions:west of the Isthmus and east of the Isthmus.In the case of the Pleistocene,the TMCFs were broken into two portions,one related to the Neotropical region and the other to the Nearctic region.Furthermore,the analyses allowed us to detect the influences of different geological and paleoclimatological events on the distribution of the TMCFs over time.Therefore,the TMCFs current distribution might have been driven by geological events during the Miocene-Pliocene,whereas climatic fluctuations have the highest impact during the Pleistocene.
文摘The relationships of Madagascan plant and animal taxa have been the object of much fascination, Madagascar sharing numerous lineages with Africa, others with Asia, Australia, or the Americas, and many others being of uncertain relationships. In commonly accepted global regionalization schemata, Madagascar is treated together with Africa for animals, and with Africa, tropical Asia and the Pacific islands in the case of plants. Here we examine the similarities between the biotic assemblages of （i） tropical Africa, （ii） Madagascar, and （iii） the rest of the world, on a basic taxonomic level, considering the families of vascular plants and vertebrates as analysis units. The percentages of endemic families, families shared pair-wise between regions, or pre- sent in all three, are roughly similar between the two broad groups, though plant families with ranges limited to one region are proportionally fewer. In dendrograms and multidimensional scaling plots for different groups, Madagascar clusters together with Africa, Asia or both, and sometimes with smaller Indian Ocean Islands, but quite often （though not in plants） as a convincingly separate cluster. Our results for vertebrates justify the status of full zoogeographic region for Madagascar, though an equally high rank in geobotanical regionalization would mean also treating Africa and Tropical Asia as separate units, which would be debata- ble given the overall greater uniformity of plant assemblages. Beyond the Madagascan focus of this paper, the differences be- tween plant and vertebrate clusters shown here suggest different levels of ecological plasticity at the same taxonomic level, with plant families being much more environmentally-bound, and thus clustering along biome lines rather than regional lines [Current Zoology 58 （3）： 363-374, 2012].
文摘Based on a cladistic biogeographic analysis of 6 species-level phylogenies of harvestman taxa, wesearched for congruence in the historical relationships of 12 areas of endemism of the BrazilianAtlantic Rain Forest. We constructed general area cladograms using Primary Brooks ParsimonyAnaJysis （BPA）, BPA of nodes, and paralogy-free subtree analysis. These analyses resulted in 6general area cladograms, that allow to infer a general pattern of the relationships among areas ofendemism from the Brazilian Atlantic Rain Forest. Northern areas resulted related basally showingmain disjunctions at the Doce River Valley and Todos os Santos Bay/S^o Francisco River Valley.The remaining areas of endemism were included in a southern and a southeastern block, sepa-rated by the Ribeira do Iguape Valley. Incongruence Length Differences tests showed no significantincongruence among the resulting cladograms and other matrix partitions. We concluded that tec-tonism and ancient marine transgressions were the probable processes responsible for the maindisjunctions, whereas Neogene refugia seem to have caused the more recent disjunctions. Thegeneral pattern and redundancy in area relationships suggest a model of main reiterative barriersin diversification at multiple times for the evolution of the Atlantic Rain Forest. The renewal of cla-distic biogeography and the search for common biogeographic patterns are discussed.
文摘Molecular dating techniques require the use of calibrations, which are usually fossil or geological vicariance-based. Fossil calibrations have been criticised because they result only in minimum age estimates. Based on a historical biogeographic perspective, I suggest that vicariance-based calibrations are more dangerous. Almost all analytical methods in historical biogeog- raphy are strongly biased towards inferring vicariance, hence vicariance identified through such methods is unreliable. Other studies, especially of groups found on Gondwanan fragments, have simply assumed vicariance. Although it was previously be- lieved that vicariance was the predominant mode of speciation, mounting evidence now indicates that speciation by dispersal is common, dominating vicaziance in several groups. Moreover, the possibility of speciation having occurred before the said geo- logical event cannot be precluded. Thus, geological calibrations can under- or overestimate times, whereas fossil calibrations al- ways result in minimum estimates. Another major drawback of vicariant calibrations is the problem of circular reasoning when the resulting estimates are used to infer ages of biogeographic events. I argue that fossil-based dating is a superior alternative to vicariance, primarily because the strongest assumption in the latter, that speciation was caused by the said geological process, is more often than not the most tenuous. When authors prefer to use a combination of fossil and vicariant calibrations, one suggestion is to report results both with and without inclusion of the geological constraints. Relying solely on vicariant calibrations should be strictly avoided
