Figures
Explore figures and images from publications
FIGURE 3 - uploaded by Nicholas Matzke
Content may be subject to copyright.
Cartoon of the likelihood terms. The biogeographic history for lineage i includes the lineage start at time (i)  

Cartoon of the likelihood terms. The biogeographic history for lineage i includes the lineage start at time (i)  

Source publication
Article
Full-text available
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...

Context in source publication

Context 1
... likelihood of the biogeographic history over all branches of the phylogeny is then simply calculated as the product of all stepwise likelihoods (Fig. ...

Citations

... R package (BioGeography with Bayesian (and likelihood) Evolutionary Analysis in R Scripts) (Matzke, 2013;Matzke & Sidje, 2013;R Core Team, 2016) combined to the ultrametric species tree obtained in BEAST to reconstruct the possible center of origin, biogeographic scenarios and possible occupation routes of the five lineages within U. superciliosus. We performed six independent analyses comparing distinct alternative models under the Akaike Information Criterion corrected (AICc): (1) Bayesian Inference of Biogeography for Discrete Areas (BayArea; Landis et al., 2013); (2) Dispersal-Vicariance Analysis (DIVA; Ronquist, 1997); and (3) Dispersal-Extinction Cladogenesis (DEC; Ree & Smith, 2008) and implementing the founder event speciation with the " + J" for all three models. We defined five biogeographic areas based on the current distribution range of each of the five lineages, limiting to both banks of the Tapajós and Madeira Rivers, the course of the Solimões River, the course of the Purus River, the North of the Amazon River, and east of Xingu River (including Marajó Island). ...
Article
Full-text available
Wetlands are present in different parts of the globe, holding a significant portion of the local biodiversity, and have been under the constant influence of climatic changes worldwide on different time scales. Investigations with a phylogeographic approach have revealed the role of Quaternary climatic shifts on a global scale, favoring constant changes in the amplitude of floodplains and affecting the evolutionary history of multi-taxa. This pattern was observed in the Amazonian biota, but due to the complex geological history, some of these models alone are insufficient, especially in widespread species that live in specific regions of the biome. Herein, we investigated the species delimitation and biogeographic history of the semi-aquatic lizard Uranoscodon superciliosus (U. superciliosus), widely distributed in Amazonian floodplains, a habitat that was for a long time considered a corridor to gene flow. Our results support a high genetic diversity with five well-supported lineages within U. superciliosus: North of the Amazon River, East Xingu, Solimões, Purus, and Tapajós-Madeira, with the basal split within this group in the Miocene and others in the Plio-Pleistocene. These results corroborated a mixture of distinct processes that shaped the diversity of U. superciliosus with rivers as vicariant barriers and the already known role of paleoclimatic shifts during the Quaternary promoting diversification. Among tetrapods, our work is one of the first to describe the genetic structure in a widespread taxon along river-edge environments, thus supporting both patterns of diversification with the compartmentalized lineages along different Amazonian rivers (floodplains) and also the more common pattern found in upland forest species, with main rivers acting as vicariant barriers and playing a role in allopatric speciation.
... the BAYAREALIKE (+J) model, based onLandis et al. (2013). We identified the best-fit model using the AIC c score.2.2.2 | ApproximateBayesian computation of the SSR data To clarify population divergence and migration histories in five island populations of M. dodecapetala (i.e. ...
Article
Full-text available
Aim: Islands are 'nature's laboratories of evolution'. Most island biogeographical studies have focussed on remote volcanic island chains. Here, we challenge island biogeo-graphical patterns using a slowly evolving recent colonist present on five islands in a nonlinear chronosequence island chain. Location: The Lesser Antilles (Caribbean). Taxon: Magnolia dodecapetala (Magnoliaceae). Methods: Genetic diversity was characterised using Sanger sequencing of 21 individuals amplified for 11 DNA markers, plus microsatellite data of 195 individuals geno-typed with 19 simple sequence repeat (SSR) markers. Sanger sequencing data were used to construct a Bayesian phylogenetic hypothesis, while SSR markers were used to run approximate Bayesian computation (ABC) demographic analyses and calculate population statistics. Results: Both types of molecular data support stepwise colonisation, decoupled from known island ages. The ABC analyses support a north to south migration while the Sanger sequencing data indicate a mixture of island progression rule and stepping stone dispersal. The SSR data show strong genetic structuring per island and significant inbreeding in all populations except in Saint Lucia. The lowest genetic diversity is found in the population from Saint Vincent. A high amount of genetic linkage occurs in a subpopulation from Dominica. Main Conclusions: Biogeographical patterns in the complex geological setting of the Lesser Antilles are uncovered using a slowly evolving study species. All genetic data support treating each island as distinct Management Units for conservation and call for a re-evaluation of the species limits. Inbreeding threatens the survival of island populations and the populations of Saint Vincent and Dominica represent conservation priorities.
... Additional processes incorporated into lineage-based macroevolutionary models include protracted speciation (Etienne & Rosindell, 2012), clade-wise diversity-dependent speciation or extinction Mahler et al., 2010), inter-and/or intraspecific competition (Aristide & Morlon, 2019;Clarke et al., 2017;Drury et al., 2016;Xu et al., 2020), co-evolution across interacting lineages (Manceau et al., 2017) and the influence of environmental variation on macroevolutionary rates (Clavel & Morlon, 2017;Condamine et al., 2013). Some of these models include the modelling of dispersal events (Goldberg et al., 2011;Landis et al., 2013Landis et al., , 2021Ree et al., 2005) and can be co-opted to make predictions about spatial patterns of biodiversity. They can potentially incorporate the effect of competition on trait evolution (Drury et al., 2018) or jointly on trait evolution and range occupancy (Quintero & Landis, 2020), allowing for the prediction of patterns of trait distribution and endemicity (for a more complete treatment of dispersal in macroevolutionary models, see Hackel & Sanmartín, 2021). ...
Article
Full-text available
MacArthur and Wilson's theory of island biogeography has been a foundation for obtaining testable predictions from models of community assembly and for developing models that integrate across scales and disciplines. Historically, however, these developments have focused on integration across ecological and macroevolutionary scales and on predicting patterns of species richness, abundance distributions, trait data and/or phylogenies. The distribution of genetic variation across species within a community is an emerging pattern that contains signatures of past population histories, which might provide an historical lens for the study of contemporary communities. As intraspecific genetic diversity data become increasingly available at the scale of entire communities, there is an opportunity to integrate microevolutionary processes into our models, moving towards development of a genetic theory of island biogeography. We aim to promote the development of process‐based biodiversity models that predict community genetic diversity patterns together with other community‐scale patterns. To this end, we review models of ecological, microevolutionary and macroevolutionary processes that are best suited to the creation of unified models, and the patterns that these predict. We then discuss ongoing and potential future efforts to unify models operating at different organizational levels, with the goal of predicting multidimensional community‐scale data including a genetic component. Our review of the literature shows that despite recent efforts, further methodological developments are needed, not only to incorporate the genetic component into existing island biogeography models, but also to unify processes across scales of biological organization. To catalyse these developments, we outline two potential ways forward, adopting either a top‐down or a bottom‐up approach. Finally, we highlight key ecological and evolutionary questions that might be addressed by unified models including a genetic component and establish hypotheses about how processes across scales might impact patterns of community genetic diversity.
... BioGeoBEARS infers ancestral geographic distributions of ancestral species and explores the role of each biogeographic event with a maximum likelihood algorithm. We compared three types of models: (i) a likelihood version of the Dispersal-Vicariance model (DIVALIKE; Ronquist, 1997; (ii) a likelihood version of the BayArea (BBM) model (Landis et al., 2013); and (iii) the Dispersal Extinction Cladogenesis model (DEC; Ree & Smith, 2008). We also compared versions of these models allowing jump dispersal, using the þJ parameter, mindful of the debate about the use of this parameter in biogeographical inference (Klaus & Matzke, 2020;Ree & Sanmart ın, 2018;Matzke, 2022). ...
Article
Determining the relative importance of dispersal and vicariance events across neotropical regions is a major goal in biogeography. These events are thought to be related to important landscape changes, notably the transition of Amazonia toward its modern hydrological configuration ca. 10 million years ago. We investigated the spatio-temporal context of the diversification of one of the major lineages of Pristimantis, a widespread and large genus of direct-developing Neotropical frogs. We gathered a spatially and taxonomically extensive sampling of mitochondrial DNA sequences from 754 Pristimantis gr. conspicillatus specimens, which led to delimiting 75 Operational Taxonomic Units (OTUs). Complete mitogenomes of 35 of these OTUs were assembled and collated with two nuDNA loci to reconstruct a time-calibrated phylogeny. We identified five major clades that diverged around the Oligocene-Miocene transition and that are largely restricted to distinct Neotropical regions i.e. Western Amazonia (P. conspicillatus clade), the Brazilian Shield (P. fenestratus clade), the Atlantic Forest (P. ramagii clade), the Guiana Shield (P. vilarsi clade) and the northern Andes (P. nicefori clade). The majority of the diversification events within these clades occurred in-situ from the early Miocene onward. Yet, a few ancient dispersal/vicariance events are inferred to have occurred among trans-Andean forests, the Atlantic Forest, the Brazilian and the Guiana Shields, but almost none in the last 10 Ma. The radical landscape transformations during the Miocene caused by the Andean orogeny and hydrological barriers such as the Pebas System and the subsequent transcontinental configuration of the Amazon drainage is a likely explanation for the isolation of the different clades within the P. gr. conspicillatus.
... The best-fitting model was BAYAREA+J (Akaike weight = 1) (SI Appendix, Table S5). The BAYAREA class of models (41), which we suggest is the class most applicable to marine organisms, differs from alternative models by allowing a widespread parent lineage to split into two widespread daughter species (SI Appendix, Extended Biogeographic Results and Discussion). This is important because most deep-sea fishes span both shallow and deep zones of the ocean (SI Appendix, Table S1). ...
... We compared the fit of six alternative models using Akaike weights (106). These were: DEC (107), DIVA-LIKE (108), BAYAREA-LIKE (41), and their equivalents with the +J parameter (cladogenetic dispersal) (20). See SI Appendix, Extended Biogeographic Results and Discussion for detailed comparison of these models in the context of bathymetric range. ...
Article
The deep sea contains a surprising diversity of life, including iconic fish groups such as anglerfishes and lanternfishes. Still, >65% of marine teleost fish species are restricted to the photic zone <200 m, which comprises less than 10% of the ocean's total volume. From a macroevolutionary perspective, this paradox may be explained by three hypotheses: 1) shallow water lineages have had more time to diversify than deep-sea lineages, 2) shallow water lineages have faster rates of speciation than deep-sea lineages, or 3) shallow-to-deep sea transition rates limit deep-sea richness. Here we use phylogenetic comparative methods to test among these three non-mutually exclusive hypotheses. While we found support for all hypotheses, the disparity in species richness is better described as the uneven outcome of alternating phases that favored shallow or deep diversification over the past 200 million y. Shallow marine teleosts became incredibly diverse 100 million y ago during a period of warm temperatures and high sea level, suggesting the importance of reefs and epicontinental settings. Conversely, deep-sea colonization and speciation was favored during brief episodes when cooling temperatures increased the efficiency of the ocean's carbon pump. Finally, time-variable ecological filters limited shallow-to-deep colonization for much of teleost history, which helped maintain higher shallow richness. A pelagic lifestyle and large jaws were associated with early deep-sea colonists, while a demersal lifestyle and a tapered body plan were typical of later colonists. Therefore, we also suggest that some hallmark characteristics of deep-sea fishes evolved prior to colonizing the deep sea.
... Outgroups were also pruned for the analysis. Ree et al. 2005), DIVALIKE ('Dispersal-Vicariance analysis' based on Ronquist 1997) and BAYAREALIKE ('Bayesian biogeographic inference for discrete areas' based on Landis et al. 2013) models. These models describe different biogeographic scenarios for anagenetic and cladogenetic range changes along the branches of a phylogenetic tree by means of the parameters: 'd' (dispersal, range expansion) and 'e' (extinction, range contraction). ...
Article
Full-text available
Unravelling the evolutionary history of taxa requires solid delimitation of the traits characterising these. This can be challenging especially in groups with a highly complex taxonomy. The squat lobster family Munididae contains more than 450 species distributed among 21 genera, Munida being the most speciose (~300 species). Previous phylogenetic studies, based on a small part of the diversity of the group, have suggested polyphyletic origins for Munida and the paraphyly of Munididae. Here, we use an integrative approach based on multi-locus phylogenies (two mitochondrial and three nuclear markers) paired with 120 morphological characters, to resolve taxonomic and evolutionary relationships within Munididae. Our study covers ~60% of the family’s known diversity (over 800 specimens of 291 species belonging to 19 of the 21 genera collected from the Atlantic, Indian and Pacific oceans). Using this information, we confirm the validity of most genera, proposing new ones in cases where the genetic analyses are compatible with morphological characters. Four well-defined munidid clades were recovered, suggesting that new genera should be erected in the currently recognised Munididae (three for the genus Agononida and eleven in Munida), and the genus Grimothea is resurrected. A key to all genera of the family is presented. Molecular clock estimates and ancestral biogeographic area reconstructions complement the taxonomic profiles and suggest some explosive diversification within Munididae during the Cretaceous and the Palaeogene. Further anagenetic events and narrow sympatry accounting for changes in distribution indicate a more limited dispersal capacity than previously considered. Our study unravels how diversification may occur in deep waters and further highlights the importance of the integrative approach in accurately delineating species in understanding the history of a family and the factors driving the evolution. ZooBank LSID: urn:lsid:zoobank.org:pub:16A61C4A-8D96-4372-820F-8EBDF179B43C
... In this study, we use probabilistic modeling of geographic range evolution, which allows users to statistically choose the number of biogeographic models based on Maximum Likelihood and Bayesian methods implemented in the R package "BioGeoBEARS" [36][37][38][39]. However, to date, no study has performed this analysis in Rhinolophidae and Hipposideridae. ...
... [39]. We statistically compared the likelihoodbased model of geographic range evolution of DEC model (Dispersal-Extinction-Cladogenesis) of LAGRANGE [41], a likelihood implementation of the processes assumed by parsimony of DIVA [42] (therefore named DIVALIKE), a likelihood version of the range evolution model of BAYAREA [37] (therefore named BAYAREA-LIKE) and a modification of DEC model by prohibiting the transition into null-range (DEC*) [38]. Each model is fully parameterized in BioGeoBEARS supermodels with different assumptions about anagenetic and cladogenetic change processes. ...
Article
Full-text available
Background Family Rhinolophidae (horseshoe bats), Hipposideridae (leaf-nosed bats) and Rhinonycteridae (trident bats) are exclusively distributed in the Old-World, and their biogeography reflects the complex historic geological events throughout the Cenozoic. Here we investigated the origin of these families and unravel the conflicting family origin theories using a high resolution tree covering taxa from each zoogeographic realm from Africa to Australia. Ancestral range estimations were performed using a probabilistic approach implemented in BioGeoBEARS with subset analysis per biogeographic range [Old-World as whole, Australia–Oriental–Oceania (AOO) and Afrotropical–Madagascar–Palearctic (AMP)]. Result Our result supports an Oriental origin for Rhinolophidae, whereas Hipposideridae originated from the Oriental and African regions in concordance with fossil evidence of both families. The fossil evidence indicates that Hipposideridae has diversified across Eurasia and the Afro-Arabian region since the Middle Eocene. Meanwhile, Rhinonycteridae (the sister family of Hipposideridae) appears to have originated from the Africa region splitting from the common ancestor with Hipposideridae in Africa. Indomalaya is the center of origin of Rhinolophidae AOO lineages, and Indomalayan + Philippines appears to be center of origin of Hipposideridae AOO lineage indicating allopatric speciation and may have involved jump-dispersal (founder-event) speciation within AOO lineage. Wallacea and the Philippines may have been used as stepping stones for dispersal towards Oceania and Australia from the Oriental region. Multiple colonization events via different routes may have occurred in the Philippines (i.e., Palawan and Wallacea) since the Late Miocene. The colonization of Rhinolophidae towards Africa from Asia coincided with the estimated time of Tethys Ocean closure around the Oligocene to Miocene (around 27 Ma), allowing species to disperse via the Arabian Peninsula. Additionally, the number of potential cryptic species in Rhinolophidae in Southeast Asia may have increased since Plio-Pleistocene and late Miocene. Conclusion Overall, we conclude an Oriental origin for Rhinolophidae, and Oriental + African for Hipposideridae. The result demonstrates that complex historical events, in addition to species specific ecomorphology and specialization of ecological niches may shape current distributions.
... and from Antonelli et al. (2018). We tested three biogeographic models that are implemented in the package within a maximum likelihood framework to detect biases amongst tested methods: Dispersal-Extinction-Cladogenesis (DEC) (Ree and Smith, 2008), a likelihood interpretation of parsimony DIVA model ('DIVALIKE'; Ronquist, 1997), and a maximum likelihood interpretation of the Bayesian-framework model implemented in the software BayArea ('BAYAREALIKE'; Landis et al., 2013). While all three models use two free parameters of anagenetic change of range evolution (dispersal and extirpation rates), they differ in how they model cladogenetic inheritance of the ancestral ranges (Matzke, 2018). ...
Article
Full-text available
Most of the unique and diverse vertebrate fauna that inhabits Madagascar derives from in situ diversification from colonisers that reached this continental island through overseas dispersal. The endemic Malagasy Scincinae lizards are amongst the most species-rich squamate groups on the island. They colonised all bioclimatic zones and display many ecomorphological adaptations to a fossorial (burrowing) lifestyle. Here we propose a new phylogenetic hypothesis for their diversification based on the largest taxon sampling so far compiled for this group. We estimated divergence times and investigated several aspects of their diversification (diversification rate, body size and fossorial lifestyle evolution, and biogeography). We found that diversification rate was constant throughout most of the evolutionary history of the group, but decreased over the last 6–4 million years and independently from body size and fossorial lifestyle evolution. Fossoriality has evolved from fully quadrupedal ancestors at least five times independently, which demonstrates that even complex morphological syndromes – in this case involving traits such as limb regression, body elongation, modification of cephalic scalation, depigmentation, and eyes and ear-opening regression – can evolve repeatedly and independently given enough time and eco-evolutionary advantages. Initial diversification of the group likely occurred in forests, and the divergence of sand-swimmer genera around 20 Ma appears linked to a period of aridification. Our results show that the large phenotypic variability of Malagasy Scincinae has not influenced diversification rate and that their rich species diversity results from a constant accumulation of lineages through time. By compiling large geographic and trait-related datasets together with the computation of a new time tree for the group, our study contributes important insights on the diversification of Malagasy vertebrates.
... 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). ...
Article
Full-text available
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). ...
Article
Full-text available
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.