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
Bangiales is the only order of the Bangiophyceae and has been suggested to be monophyletic. This order contains approximately 190 species and is distributed worldwide. Previous molecular studies have produced robust p...Bangiales is the only order of the Bangiophyceae and has been suggested to be monophyletic. This order contains approximately 190 species and is distributed worldwide. Previous molecular studies have produced robust phylogenies among the red algae, but the divergence times, historical biogeography and evolutionary rates of Bangiales have rarely been studied. Phylogenetic relationships within the Bangiales were examined using the concatenated gene sets from all available organellar genomes. This analysis has revealed the topology((( Bangia, Porphyra) Pyropia) Wildemania). Molecular dating indicates that Bangiales diversifi ed approximately 246.40 million years ago(95% highest posterior density(HPD)= 194.78–318.24 Ma, posterior probability(PP)=0.99) in the Late Permian and Early Triassic, and that the ancestral species most likely originated from eastern Gondwanaland(currently New Zealand and Australia) and subsequently began to spread and evolve worldwide. Based on pairwise comparisons, we found a slower rate of nucleotide substitutions and lower rates of diversifi cation in Bangiales relative to Florideophyceae. Compared with Viridiplantae(green algae and land plants), the evolutionary rates of Bangiales and other Rhodophyte groups were found to be dramatically faster, by more than 3-fold for plastid genome(ptDNA) and 15-fold for mitochondrial genome(mtDNA). In addition, an average 2.5-fold lower dN/dS was found for the algae than for the land plants, which indicates purifying selection of the algae.展开更多
Biogeography of the leaflaopper subfamily Stegelytrinae Baker is studied based on an analysis of geographical distribution of this subfamily worldwide using a cluster analysis of the zoological distribution of areas o...Biogeography of the leaflaopper subfamily Stegelytrinae Baker is studied based on an analysis of geographical distribution of this subfamily worldwide using a cluster analysis of the zoological distribution of areas of endemism as well as the phylogeny of representatives of this subfamily. Results show that the Stegelytrinae mainly occur in the Oriental Region and in the Mediterranean area of the Palaearctic Region, and this extends to the east side of both Wallaee＇s and Weber＇s lines. Eleven areas of endemism of this subfamily are recognized. The proportions of endemic taxa in different areas of endemism are generally very high in comparison with other leaflaopper groups, but distinct differences could be found among the different areas of endemism of Stegelytrinae. This subfamily is most intensively diversified in the Indochina Peninsula （INCN）. This is the stegelytrine distribution center, having the highest biodiversity at both genetic and species levels. The dendrogram of endemic areas of Stegelytrinae constructed using cluster analysis of the zoological distribution of Stegelytrinae at generic level shows the endemic areas of Stegelytrinae can be divided into 4 large groups. Relationships among different endemic areas of Stegelytrinae correspond largely to the geologic history of related areas, which indicates that the evolution and vicariance of this subfamily have been closely related to the history of continental drift and climate changes. It is deduced that the presumed monophyletic Stegelytrinae originated in the Oriental Region after North America had separated from Eurasia; this is the case in the monophyletic genera group which is supported by the lateral frontal sutures extending dorsally well beyond the corresponding ocellus. In addition, two expanding traces of the Stegelytrinae are presumed, which remain plausible explanations for the dispersal of Stegelytrinae： （1） New Guinea （and probably （＋ Australia）） - Kalimantan - Sumatra - Malay Peninsula - Indochina Peninsula - Central and Southern China - （Southwestern China ＋ Nepal ＋ Northeastern India） - （Northwestern India ＋ Eastern Afghanistan）; and （2） Indochina Peninsula- Central and Southern China- （Western Asia ＋ Mediterranean Sea coastal area）.展开更多
Unraveling the diversification mechanisms of organisms is a fundamental and important macroevolutionary question regarding the diversity,ecological niche, and morphological divergence of life. However, many studies ha...Unraveling the diversification mechanisms of organisms is a fundamental and important macroevolutionary question regarding the diversity,ecological niche, and morphological divergence of life. However, many studies have only explored diversification mechanisms via isolated factors. Here,based on comparative phylogenetic analysis, we performed a macroevolutionary examination of horseshoe bats(Chiroptera: Rhinolophidae:Rhinolophus), to reveal the inter-relationships among diversification, intrinsic/extrinsic factors, and climatic ecological niche characteristics. Results showed a general slowing trajectory during diversification, with two dispersal events from Asia into Southeast Asia and Africa playing key roles in shaping regional heterogeneous diversity. Morphospace expansions of the investigated traits(e.g., body size,echolocation, and climate niche) revealed a decoupled pattern between diversification trajectory and trait divergence, suggesting that other factors(e.g., biotic interactions) potentially played a key role in recent diversification. Based on ancestral traits and pathway analyses, most Rhinolophus lineages belonging to the same region overlapped with each other geographically and were positively associated with the diversification rate, implying a competitive prelude to speciation. Overall, our study showed that multiple approaches need to be integrated to address diversification history. Rather than a single factor, the joint effects of multiple factors(biogeography, environmental drivers, and competition) are responsible for the current diversity patterns in horseshoe bats, and a corresponding multifaceted strategy is recommended to study these patterns in the future.展开更多
A plethora of studies investigating the origin and evolution of diverse mountain taxa has assumed a causal link between geological processes （orogenesis） and a biological response （diversification）. Yet, a substan...A plethora of studies investigating the origin and evolution of diverse mountain taxa has assumed a causal link between geological processes （orogenesis） and a biological response （diversification）. Yet, a substantial delay （up to 30 Myr） between the start of orogenesis and diversification is often observed. Evolutionary biologists should therefore identify alternative drivers of diversification and maintenance of biodiversity in mountain systems. Using phylogenetic, biogeographic, and diversification rate analyses, we could identify two independent processes that most likely explain the diversity of the widespread genus Allium in the Qinghai-Tibet Plateau （QTP） region： （1） While the QTP-related taxa of the subgenus Melanocrommyum diversified in situ, （2） QTP-related taxa of other subgenera migrated into the QTP from multiple source areas. Furthermore, shifts in diversification rates within Allium could not be attributed spatially and temporally to the uplift history of the QTP region. Instead, global cooling and climate oscillations in the Quaternary were major contributors to increased speciation rates in three clades of AUium. Our study therefore adds to the growing evidence supporting the ＂mountain-geo-biodiversity hypothesis＂, which highlights the role of climate oscillations for the diversification of mountain organisms.展开更多
Phylogenomic evidence from an increasing number of studies has demonstrated that different data sets and analytical approaches often reconstruct strongly supported but conflicting relationships.In this study,785 singl...Phylogenomic evidence from an increasing number of studies has demonstrated that different data sets and analytical approaches often reconstruct strongly supported but conflicting relationships.In this study,785 single-copy nuclear genes and 75 complete plastomes were used to infer the phylogenetic relationships and estimate the historical biogeography of the apple genus Malus sensu lato,an economically important lineage disjunctly distributed in the Northern Hemisphere and involved in known and suspected hybridization and allopolyploidy events.The nuclear phylogeny recovered the monophyly of Malus s.l.(including Docynia);however,the genus was supported to be biphyletic in the plastid phylogeny.An ancient chloroplast capture event in the Eocene in western North America best explains the cytonuclear discordance.Our conflict analysis demonstrated that ILS,hybridization,and allopolyploidy could explain the widespread nuclear gene tree discordance.One deep hybridization event(Malus doumeri)and one recent event(Malus coronaria)were detected in Malus s.l.Furthermore,our historical biogeographic analysis integrating living and fossil data supported a widespread East Asianwestern North American origin of Malus s.l.in the Eocene,followed by several extinction and dispersal events in the Northern Hemisphere.We also propose a general workflow for assessing phylogenomic discordance and biogeographic analysis using deep genome skimming data sets.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Supported by the National Natural Science Foundation of China(No.31372517)the Scientific and Technological Innovation Project supported by the Qingdao National Laboratory for Marine Science and Technology(No.2015ASKJ02)the National Infrastructure of Fishery Germplasm Resources(No.2016DKA30470)
文摘Bangiales is the only order of the Bangiophyceae and has been suggested to be monophyletic. This order contains approximately 190 species and is distributed worldwide. Previous molecular studies have produced robust phylogenies among the red algae, but the divergence times, historical biogeography and evolutionary rates of Bangiales have rarely been studied. Phylogenetic relationships within the Bangiales were examined using the concatenated gene sets from all available organellar genomes. This analysis has revealed the topology((( Bangia, Porphyra) Pyropia) Wildemania). Molecular dating indicates that Bangiales diversifi ed approximately 246.40 million years ago(95% highest posterior density(HPD)= 194.78–318.24 Ma, posterior probability(PP)=0.99) in the Late Permian and Early Triassic, and that the ancestral species most likely originated from eastern Gondwanaland(currently New Zealand and Australia) and subsequently began to spread and evolve worldwide. Based on pairwise comparisons, we found a slower rate of nucleotide substitutions and lower rates of diversifi cation in Bangiales relative to Florideophyceae. Compared with Viridiplantae(green algae and land plants), the evolutionary rates of Bangiales and other Rhodophyte groups were found to be dramatically faster, by more than 3-fold for plastid genome(ptDNA) and 15-fold for mitochondrial genome(mtDNA). In addition, an average 2.5-fold lower dN/dS was found for the algae than for the land plants, which indicates purifying selection of the algae.
基金supported by the National Natural Science Foundation of China(30970389)
文摘Biogeography of the leaflaopper subfamily Stegelytrinae Baker is studied based on an analysis of geographical distribution of this subfamily worldwide using a cluster analysis of the zoological distribution of areas of endemism as well as the phylogeny of representatives of this subfamily. Results show that the Stegelytrinae mainly occur in the Oriental Region and in the Mediterranean area of the Palaearctic Region, and this extends to the east side of both Wallaee＇s and Weber＇s lines. Eleven areas of endemism of this subfamily are recognized. The proportions of endemic taxa in different areas of endemism are generally very high in comparison with other leaflaopper groups, but distinct differences could be found among the different areas of endemism of Stegelytrinae. This subfamily is most intensively diversified in the Indochina Peninsula （INCN）. This is the stegelytrine distribution center, having the highest biodiversity at both genetic and species levels. The dendrogram of endemic areas of Stegelytrinae constructed using cluster analysis of the zoological distribution of Stegelytrinae at generic level shows the endemic areas of Stegelytrinae can be divided into 4 large groups. Relationships among different endemic areas of Stegelytrinae correspond largely to the geologic history of related areas, which indicates that the evolution and vicariance of this subfamily have been closely related to the history of continental drift and climate changes. It is deduced that the presumed monophyletic Stegelytrinae originated in the Oriental Region after North America had separated from Eurasia; this is the case in the monophyletic genera group which is supported by the lateral frontal sutures extending dorsally well beyond the corresponding ocellus. In addition, two expanding traces of the Stegelytrinae are presumed, which remain plausible explanations for the dispersal of Stegelytrinae： （1） New Guinea （and probably （＋ Australia）） - Kalimantan - Sumatra - Malay Peninsula - Indochina Peninsula - Central and Southern China - （Southwestern China ＋ Nepal ＋ Northeastern India） - （Northwestern India ＋ Eastern Afghanistan）; and （2） Indochina Peninsula- Central and Southern China- （Western Asia ＋ Mediterranean Sea coastal area）.
基金supported by the National Natural Science Foundation of China(31970394,32192421,31300314)Special Foundation for National Science and Technology Basic Research Program of China(2021FY100303)。
文摘Unraveling the diversification mechanisms of organisms is a fundamental and important macroevolutionary question regarding the diversity,ecological niche, and morphological divergence of life. However, many studies have only explored diversification mechanisms via isolated factors. Here,based on comparative phylogenetic analysis, we performed a macroevolutionary examination of horseshoe bats(Chiroptera: Rhinolophidae:Rhinolophus), to reveal the inter-relationships among diversification, intrinsic/extrinsic factors, and climatic ecological niche characteristics. Results showed a general slowing trajectory during diversification, with two dispersal events from Asia into Southeast Asia and Africa playing key roles in shaping regional heterogeneous diversity. Morphospace expansions of the investigated traits(e.g., body size,echolocation, and climate niche) revealed a decoupled pattern between diversification trajectory and trait divergence, suggesting that other factors(e.g., biotic interactions) potentially played a key role in recent diversification. Based on ancestral traits and pathway analyses, most Rhinolophus lineages belonging to the same region overlapped with each other geographically and were positively associated with the diversification rate, implying a competitive prelude to speciation. Overall, our study showed that multiple approaches need to be integrated to address diversification history. Rather than a single factor, the joint effects of multiple factors(biogeography, environmental drivers, and competition) are responsible for the current diversity patterns in horseshoe bats, and a corresponding multifaceted strategy is recommended to study these patterns in the future.
基金the German Research Foundation for funding of staff (project no. MU 2934/2-1)the support of the German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig funded by the German Research Foundation (FZT 118) for funding of lab expenses
文摘A plethora of studies investigating the origin and evolution of diverse mountain taxa has assumed a causal link between geological processes （orogenesis） and a biological response （diversification）. Yet, a substantial delay （up to 30 Myr） between the start of orogenesis and diversification is often observed. Evolutionary biologists should therefore identify alternative drivers of diversification and maintenance of biodiversity in mountain systems. Using phylogenetic, biogeographic, and diversification rate analyses, we could identify two independent processes that most likely explain the diversity of the widespread genus Allium in the Qinghai-Tibet Plateau （QTP） region： （1） While the QTP-related taxa of the subgenus Melanocrommyum diversified in situ, （2） QTP-related taxa of other subgenera migrated into the QTP from multiple source areas. Furthermore, shifts in diversification rates within Allium could not be attributed spatially and temporally to the uplift history of the QTP region. Instead, global cooling and climate oscillations in the Quaternary were major contributors to increased speciation rates in three clades of AUium. Our study therefore adds to the growing evidence supporting the ＂mountain-geo-biodiversity hypothesis＂, which highlights the role of climate oscillations for the diversification of mountain organisms.
基金National Natural Science Foundation of China supports this research (32000163 and 31620103902)
文摘Phylogenomic evidence from an increasing number of studies has demonstrated that different data sets and analytical approaches often reconstruct strongly supported but conflicting relationships.In this study,785 single-copy nuclear genes and 75 complete plastomes were used to infer the phylogenetic relationships and estimate the historical biogeography of the apple genus Malus sensu lato,an economically important lineage disjunctly distributed in the Northern Hemisphere and involved in known and suspected hybridization and allopolyploidy events.The nuclear phylogeny recovered the monophyly of Malus s.l.(including Docynia);however,the genus was supported to be biphyletic in the plastid phylogeny.An ancient chloroplast capture event in the Eocene in western North America best explains the cytonuclear discordance.Our conflict analysis demonstrated that ILS,hybridization,and allopolyploidy could explain the widespread nuclear gene tree discordance.One deep hybridization event(Malus doumeri)and one recent event(Malus coronaria)were detected in Malus s.l.Furthermore,our historical biogeographic analysis integrating living and fossil data supported a widespread East Asianwestern North American origin of Malus s.l.in the Eocene,followed by several extinction and dispersal events in the Northern Hemisphere.We also propose a general workflow for assessing phylogenomic discordance and biogeographic analysis using deep genome skimming data sets.
