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Historical biogeography is increasingly studied from an explicitly statistical perspective, using stochastic models to describe the evolution of species range as a continuous-time Markov process of dispersal between and extinction within a set of discrete geographic areas. The main constraint of these methods is the computational limit on the numbe...

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... com/ nmatz ke/ BioGe oBEARS) to infer the ancestral areas for Fouquieria. We undertook a maximum likelihood analysis under six different biogeographic models as follows: a) DEC (dispersal-extinction-cladogenesis; Ree and Smith 2008), b) DIVALIKE (a likelihood interpretation of the Dispersal Vicariance Analysis, DIVA; Ronquist 1997), and c) BAYAREALIKE (a likelihood interpretation of BayArea; Landis et al. 2013). All of these models include anagenetic and cladogenetic processes, in which "dispersal" is modeled as an anagenetic range-expansion process (rate parameter d), while "extinction" is modeled as an anagenetic range-contraction process (rate parameter e). ...
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Fouquieriaceae consists of a single genus Fouquieria with eleven species occurring in arid and semiarid regions in Mexico and the southwestern USA. A recently developed phylogeny based on chloroplast DNA sequences provided strong support for the monophyly of the genus and the evolutionary species relationships. However, details of its evolutionary history remain unclear. Due to this uncertainty, additional information such as the evolution on its growth habit, reconstruction of the ancestral habitat, and on chromosome evolution is needed for a clear understanding of its evolutionary history. Different hypotheses concerning the shift of growth habits (succulent or woody) and the occupation of the ancestral habitat, and the chromosomal evolution in the family were analyzed. We assessed the ancestral distribution by fitting different biogeographic models. Our results suggest that Fouquieriaceae may have originated in two regions at the margins of the present geographic distribution of the genus: the Sonoran Desert and desert areas south of the Mexican Transvolcanic Belt. However, our results suggest that the ancestral lineage of Foquieriaceae was originated in desert habitats in central–southern Mexico with a basal chromosome number of n = 12, and a succulent habit, all of which may have allowed the dispersion of polyploid species to newly developed dry environments during the Late Miocene.
... We used "BioGeoBEARS" to calculate the log-likelihood (lnL) and the corrected Akaike Information Criterion (AICc) to choose the best fitting biogeographical model. For this we considered the six "BioGeoBEARS" models: likelihood-based Dispersal-Extinction Cladogenesis (Ree and Smith 2008;Matzke 2013b), and DEC considering founder-event (Matzke 2013b(Matzke , 2014; DIVAlike, a likelihood version of the DIVA model (Ronquist and Sanmartín 2011), and DIVAlike considering founder-event (DIVAlike + J -Matzke 2013b, 2014); and BAYAREAlike which is a likelihood version of the BAYAREA (Landis et al. 2013), and BAYAREAlike considering founder-event (BAYAREAlike + J -Matzke 2013b, 2014). The DEC model presumes that lineages that derived after cladogenesis will inherit a single-range area, which can be a subset of the ancestor's range. ...
... The DIVAlike model permits derived lineages to inherit more than one area as their range, but it cannot be a subset of the ancestor's range (Ronquist and Sanmartín 2011). The BAYAREAlike presumes that at cladogenesis there is no range evolution, i.e. that the derived lineages inherit the same range of the ancestral state (Landis et al. 2013). The parameter "J" adds founder-event to each of the mentioned models (DEC + J, DIVAlike + J, and BAYA-REAlike + J -Matzke 2013b, 2014). ...
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Pontoporia blainvillei (Gervais & d’Orbigny, 1844), the franciscana dolphin, is the most endangered small cetacean in the Western South Atlantic. It is an endemic species with a coastal and estuarine distribution that has been divided into four Franciscana Management Areas (FMAs). We used the mitochondrial DNA control region to conduct a phylogeographic analysis to evaluate the population structure of the franciscana and the influence of paleoceanographic events on its biogeographic history. We found nine populations along the entire distribution (ΦST = 0.41, ΦCT = 0.38, p < 10–5), with estimated migration rates resulting in less than one female per generation. Populations from FMAIII and FMAIV in the south (including the Río de La Plata Estuary) showed higher long-term migration rates and effective population sizes than northern populations. The phylogeographic analysis supports the franciscana origin in the Río de La Plata Estuary, with further dispersal south and northwards. The first lineage split happened around 2.5 Ma, with lineage radiation throughout the Pleistocene until recent fragmentation events shaped current-day populations. We suggest that Pleistocene glaciations influenced the dispersion and population structure of the franciscana. Specifically, that the shift of the Brazil-Malvinas Confluence drove the dispersion northwards. Then, low sea-level periods caused either the isolation in estuarine refugia or local extinctions, followed by re-colonizations.
... Here, we inserted the coordinates of each estimated ancestral range (A-F) as our input data in the S-DEC parameters setup, and included the locations of the oldest fossil to calculate the probability of ancestral range for each ancestral clade. To obtain the most probable area as the range of ancestry for each recovered clade, we computed a Bayesian inference analysis for discrete areas (BAYarea; Landis et al. 2013) on the condensed time trees, with 10 million MCMC generations and a burn in of 500,000 generations. ...
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Landscape structures drive biogeographic patterns and population connectivity of animals distributed across diverse biotopes. Here, we provide a fresh insight on the impact of five landscape types in East Asia on the phylogeography and acoustic variability of the widespread Mongolian Toad, Strauchbufo raddei. For the first time, we reconstructed the biogeography of S. raddei over the species’ entire range throughout East Asia (N = 293; assembled up to 2,613 bp of concatenated CR-COI-12S rRNA-16S rRNA) using fossil-based molecular dating and genetic connectivity assessments. In addition, we addressed past population dynamics in relation to landscape types, and geographic variations in release calls for the clades occurring in the steppes of northern Mongolia and the Amur River basin (N = 147). Our results recovered two separate ancestors of S. raddei in East Asia, supporting a basal split between the northeastern and southern lineages in the Middle Miocene, c. 9.48 – 13.77 Mya. Ancestral range estimates suggested a Late Miocene radiation within the northeastern lineage, likely due to aridity-induced vicariance and dispersal from the central Asian steppes, c. 7.89 (5.25 – 11.50) Mya. The southern lineage emerged subsequently from glacial refugia, c. 6.84 (3.48 – 2.63) Mya, expanding northward and crossing the Gobi Desert and current-day Mongolia, c. 2.60 (1.15 – 3.72) Mya. At the exception of the pre-Tibetan Plateau clade, our reconstruction of migration trajectories highlighted the presence of effective gene flow across other landscapes, notably among the central and northeastern Chinese clades in the habitats defined as steppe, river basin and canyon. Significant variation in release calls between the clades in northern Mongolia and the Amur River Basin reflected the isolation between the two clades, and supported the presence of a northern refugium and post-glacial expansion of the southern lineage into northwestern Mongolia. In contrast with prior studies, our finding indicates that release calls can reflect phylogeographic patterns.
... Although different parametric biogeographic methods have been developed over the last 25 years (Ronquist, 1997;Ree et al., 2005;Landis et al., 2013;Matzke, 2014;Dupin et al., 2017), their adoption to test evolutionary-based hypotheses underlying geographical diversity gradients has been slow (but see Böhm and Mayhew, 2005 for an early exemplar). Some recent studies have utilized them (Kennedy et al., 2017;Miller and Román-Palacios, 2021), but methodological limitations still remain. ...
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The intersection of macroecology and macroevolution is one of today's most active research in biology. In the last decade, we have witnessed a steady increment of macroecological studies that use metrics attempting to capture macroevolutionary processes to explain present-day biodiversity patterns. Evolutionary explanations of current species richness gradients are fundamental for understanding how diversity accumulates in a region. Although multiple hypotheses have been proposed to explain the patterns we observe in nature, it is well-known that the present-day diversity patterns result from speciation, extinction, colonization from nearby areas, or a combination of these macroevolutionary processes. Whether these metrics capture macroevolutionary processes across space is unknown. Some tip-rate metrics calculated directly from a phylogenetic tree (e.g., mean root distance -MRD-; mean diversification rate -mDR-) seem to return very similar geographical patterns regardless of how they are estimated (e.g., using branch lengths explicitly or not). Model-based tip-rate metrics —those estimated using macroevolutionary mixtures, e.g., the BAMM approach— seem to provide better net diversification estimates than only speciation rates. We argue that the lack of appropriate estimates of extinction and dispersal rates in phylogenetic trees may strongly limit our inferences about how species richness gradients have emerged at spatial and temporal scales. Here, we present a literature review about this topic and empirical comparisons between select taxa with several of these metrics. We implemented a simple null model approach to evaluate whether mapping of these metrics deviates from a random sampling process. We show that phylogenetic metrics by themselves are relatively poor at capturing speciation, extinction, and dispersal processes across geographical gradients. Furthermore, we provide evidence of how parametric biogeographic methods can improve our inference of past events and, therefore, our conclusions about the evolutionary processes driving biodiversity patterns. We recommend that further studies include several approaches simultaneously (e.g., spatial diversification modeling, parametric biogeographic methods, simulations) to disentangle the relative role of speciation, extinction, and dispersal in the generation and maintenance of species richness gradients at regional and global scales.
... routes below the species level. We compared six models: dispersal-extinction-cladogenesis (DEC; Ree and Smith, 2008), dispersal-vicariance analysis (DIVA; Ronquist, 1997) and BAYAREA models (Landis et al., 2013), plus all three models separately with the possibility of founder events (+j; Matzke, 2013Matzke, , 2014. As our main objective was to trace ancestral areas rather than to infer the diversification dynamics or the speciation mode, concerns raised by Ree and Sanmartín (2018) on the DEC + J model are unlikely to have significant effects on our results. ...
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Understanding the evolutionary and ecological processes driving population differentiation and speciation can provide critical insights into the formation of biodiversity. Here, we examine the link between population genetic processes and biogeographic history underlying the generation of diversity in the Hengduan Mountains (HM), a region harboring a rich and dynamic flora. We used restriction site-associated DNA sequencing to generate 1,907 single-nucleotide polymorphisms (SNPs) and four-kb of plastid sequence in species of the Gentiana hexaphylla complex (Gentianaceae). We performed genetic clustering with spatial and non-spatial models, phylogenetic reconstructions, and ancestral range estimation, with the aim of addressing the processes influencing diversification of G. hexaphylla in the HM. We find the G. hexaphylla complex is characterized by geographic genetic structure with clusters corresponding to the South, North and the central HM. Phylogenetic reconstruction and pairwise F ST analyses showed deep differentiation between Southern and Northern populations in the HM. The population in Mount Taibai exhibited the highest genetic similarity to the North HM. Ancestral range estimation indicated that the G. hexaphylla complex originated in the central HM and then diverged in the Pliocene and the Early Pleistocene, before dispersing widely, resulting in the current distinct lineages. Overall, we found deep genomic differentiation in the G. hexaphylla complex corresponds to geographic barriers to dispersal in the HM and highlights a critical role of the uplift of the Daxue Mountains and subsequent climatic fluctuations underlying diversification. The colonization of G. hexaphylla in the Mount Taibai region suggests directional dispersal between the alpine flora of the Qinling Mountains and the HM.
... Methods used for probabilistic historical biogeographical reconstruction included Bayesian inference for discrete areas (BayAreas; Landis et al., 2013), statistical dispersalvicariance analysis (S-DIVA; Yu et al., 2010), statistical dispersal-extinction-cladogenesis (S-DEC) (Ree et al., 2005;Ree and Smith, 2008), and analysis of biogeography in RevBayes, approximately following . Each of these methods uses either maximum likelihood or Bayesian posterior estimates of the ancestral geographic ranges of internal nodes on a time calibrated phylogenetic tree, based on stepwise hindcasting from current ranges of the taxa at the tree tips (cf. ...
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Premise: The Cactaceae of northwestern Mexico and the southwestern United States constitute a major component of the angiosperm biodiversity of the region. The Mammilloid clade, (Cactaceae, tribe Cacteae), composed of the genera Cochemiea, Coryphantha, Cumarinia, Mammillaria, and Pelecyphora is especially species rich. We sought to understand the timing, geographical and climate influences correlated with expansion of the Mammilloid clade, through the Sonoran Desert into Baja California. Methods: We reconstructed the historical biogeography of the Mammilloid clade, using Bayesian and maximum likelihood methods, based on a strongly supported molecular phylogeny. We also estimated divergence times, the timing of emergence of key characters, and diversification rates and rate shifts of the Mammilloid clade. Key results: We found that the most recent common ancestor of Cochemiea arrived in the Cape region of Baja California from the Sonoran Desert region approximately 5 million years ago, coinciding with the timing of peninsular rifting from the mainland, suggesting dispersal and vicariance as causes of species richness and endemism. The diversification rate for Cochemiea is estimated to be approximately 12 times that of the mean background diversification rate for angiosperms. Divergence time estimation shows that many of the extant taxa in Cochemiea and Baja California Mammillaria emerged from common ancestors 1 million to 200,000 years ago, having a mid-Pleistocene origin. Conclusions: Cochemiea and Mammillaria of the Baja California region are examples of recent, rapid diversification. Geological and climatic forces at multiple spatial and temporal scales are correlated with the western distributions of the Mammilloid clade. This article is protected by copyright. All rights reserved.
... 1.1.2 (Matzke 2013(Matzke , 2014: 1) dispersal-extinction-cladogenesis (DEC; Ree et al. 2005, Ree andSmith 2008); 2) DIVA-like (a likelihood implementation of DIVA; Ronquist 1997); and 3) BAYAREA-like (a likelihood implementation of BayArea; Landis et al. 2013). In the 'BioGeoBEARS' implementation of these models, biogeographical movements (i.e. ...
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Understanding the role of traits in dispersal is necessary to improve our knowledge of historical biogeography, community assembly processes and predictions of species' future movements. Here we aimed to determine the relationship between three traits (coastal distribution, body size, position on the fast/slow life history continuum) and past dispersal probability on an evolutionary timescale in chameleons (Chamaeleonidae). Using species' distribution data we identified the nine most important biogeographic regions for all included chameleons (181/217 species). We compiled life history trait data and used phylogenetic factor analysis to infer independent body size and fast/slow life history trait axes. Finally, we tested whether traits and trait combinations related to biogeographic dispersal success in the past, using trait‐dependent biogeographic models. All three traits were associated with past biogeographical movements. Lineages having coastal distributions and those with large bodies had higher dispersal probabilities. Interestingly, chameleons with either a very fast or very slow life history were more successful dispersers than species with an intermediate strategy. Together, the three traits – coastal, large‐bodied and extreme life history – form a dispersal syndrome. Traits have played an important role in the biogeographic history of chameleons. While only fast traits have been linked to present‐day invasion success in reptiles, both extremes of the life history spectrum were likely advantageous for dispersal and establishment during past biogeographic movements. Fast‐living species may be less susceptible to stochastic extinction in the first phases of a colonization (due to rapid population growth), and slow‐living species may be less vulnerable to environmental stochasticity (due to low demographic variability). Our results call for broader analyses testing the general influence of life history strategy in biogeographic dispersal success, which would help explain species distribution patterns on Earth.
... These studies (Groussin et al. 2017, Satler et al. 2019) demonstrate the potential for model-based approaches to yield deeper insights into the macroevolution of ecological interactions. Braga et al. (2020) developed an approach for understanding host-repertoire evolution in clades of parasitic lineages that uses models adapted from the field of historical biogeography to describe species-area distributions (Landis et al. 2013, Ree et al. 2005. In this method, each parasitic lineage has a host repertoire, which is the set of possible hosts a parasitic species can exploit. ...
Article
Myriad branches in the tree of life are intertwined through ecological relationships. Biologists have long hypothesized that intimate symbioses between lineages can influence diversification patterns to the extent that it leaves a topological imprint on the phylogenetic trees of interacting clades. Over the past few decades, cophylogenetic methods development has provided a toolkit for identifying such histories of codiversification, yet it is often difficult to determine which tools best suit the task at hand. In this review, we organize currently available cophylogenetic methods into three categories—pattern-based statistics, event-scoring methods, and more recently developed generative model–based methods—and discuss their assumptions and appropriateness for different types of cophylogenetic questions. We classify cophylogenetic systems based on their biological properties to provide a framework for empiricists investigating the macroevolution of symbioses. In addition, we provide recommendations for the next generation of cophylogenetic models that we hope will facilitate further methods development. Expected final online publication date for the Annual Review of Ecology, Evolution, and Systematics, Volume 53 is November 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
... Ideally the root area of the outgroup should be used in the analysis but it was unknown for both cases. The selection of this method was based on a test in Bio-GeoBEARS (Matzke, 2018) in RASP that compared among the Dispersal-Vicariance Analysis (DIVA; (Ronquist and Cannatella, 1997), Dispersal-Extinction-Cladogenesis (DEC), and BayArea methods (Landis et al., 2013). We did not consider the parameter j ("jump") (Matzke, 2018) in the test, due to concerns raised in Ree and Sanmartín (2018). ...
Article
Hyb-Seq and RAD-seq are well-established high throughput sequencing technologies that have been increasingly used for plant phylogenomic studies. Each method has its own pros and cons. The choice between them is a practical issue for plant systematists studying the evolutionary histories of biodiversity of relatively recent origins. However, few studies have compared the congruence and conflict between results from the two methods within the same group of organisms in plants. In this study, we employed RAD-seq and Hyb-Seq of Angiosperms353 genes in phylogenomic and biogeographic studies of Hamamelis (the witch-hazels) and Castanea (chestnuts), two classic examples exhibiting the well-known eastern Asian (EA) -eastern North American (ENA) disjunct distribution, and compared them side by side. Our results showed congruences in phylogenetic inference and divergence time dating between the two data sets obtained through our customized procedures of library preparation and sequence trimming, although they differed in the number of loci and informative sites, the amount of missing data, and sampling within species. We provide recommendations regarding the selection of the two methods for phylogenomic study at generic level based on fund availability and sampling scale. If funds and time are not constrained, we recommend Hyb-Seq. If funds and time are somewhat limited and sampling is large, we recommend RAD-seq. However, we found greater conflict among gene trees from the RAD-seq data due to the short sequences per locus. Therefore, species tree building and network detecting with the RAD-Seq data with short RAD-seq loci (e.g., <150 bp) should avoid using analytical methods relying on gene trees of individual locus, but using site-based methods such as SVDQuartets and D-statistic method. Our phylogenetic analyses of RAD-seq and Hyb-Seq data resulted in well-resolved species relationships. Analyses of the data using the D-statistic test and PhyloNet revealed ancient introgressions in both genera. Biogeographic analyses including fossil data using total evidence-based dated tree and DEC model applying specific inter-area dispersal probabilities revealed a complicated history for each genus, indicating multiple interareal dispersals and local extinctions within and outside areas of the taxa's modern ranges in both the Paleogene and Neogene. The study demonstrates the importance of including fossil taxa for a more accurate reconstruction of biogeographic histories of taxa to understand the EA and ENA floristic disjunction. Our results support a widespread ancestral range in EA-western North America (WNA) followed by early diversification in EA and expansion to North America (NA) and Europe for Castanea and a more widespread ancestral range in EA-ENA-WNA for Hamamelis. The origins of the modern EA-ENA disjunction in both genera were suggested to be the result of vicariance from widespread ancestors in Eurasia-ENA of the mid-Miocene and in EA-NA of the late Oligocene, respectively. [RAD-seq, Hyb-Seq, Angiosperms353, Castanea, Hamamelis, biogeography, eastern Asia-eastern North America disjunction]
... Models plus a "j" parameter, representing founder event speciation, were excluded as they might be inappropriate according to the study of Ree and Sanmartín (2018). In addition, the BAYAREALIKE model in BioGeoBEARS is not suitable for our studied group and biogeographic area definitions, and thus was also excluded following several previous studies (Landis et al., 2013;Birch and Kocyan, 2021;Maguilla et al., 2021;Nge et al., 2022). ...
Article
After the merger of the former Taxodiaceae and Cupressaceae s.s., currently the conifer family Cupressaceae (sensu lato) comprises seven subfamilies and 32 genera, most of which are important components of temperate and mountainous forests. With the exception of a recently published genus-level phylogeny of gymnosperms inferred from sequence analysis of 790 orthologs, previous phylogenetic studies of Cupressaceae were based mainly on morphological characters or a few molecular markers, and did not completely resolve the intergeneric relationships. In this study, we reconstructed a robust and well-resolved phylogeny of Cupressaceae represented by all 32 genera, using 1944 genes (Orthogroups) generated from transcriptome sequencing. Reticulate evolution analyses detected a possible ancient hybridization that occurred between ancestors of two subclades of Cupressoideae, including Microbiota-Platycladus-Tetraclinis (MPT) and Juniperus-Cupressus-Hesperocyparis-Callitropsis-Xanthocyparis (JCHCX), although both concatenation and coalescent trees are highly supported. Moreover, divergence time estimation and ancestral area reconstruction indicate that Cupressaceae very likely originated in Asia in the Triassic, and geographic isolation caused by continental separation drove the vicariant evolution of the two subfamilies Cupressoideae and Callitroideae in the northern and southern hemispheres, respectively. Evolutionary analyses of some morphological characters suggest that helically arranged linear-acicular leaves and imbricate bract-scale complexes represent ancestral states, and the shift from linear-acicular leaves to scale-like leaves was associated with the shift from helical to decussate arrangement. Our study sheds new light on phylogeny and evolutionary history of Cupressaceae, and strongly suggests that both dichotomous phylogenetic and reticulate evolution analyses be conducted in phylogenomic studies.