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Gymnophthalmids are a diverse lineage of Neotropical lizards that present challenges in the understanding of their phylogenetic relationships and biogeographic history. Using a densely sampled phylogeny and distribution data, we investigated their biogeography at the family level. Dividing South and Central America into 12 regions, we tested six biogeographic models considering dispersal-extinction, vicariance, and founder events. Our analysis revealed high taxonomic and phylogenetic endemism in the Andes, Amazon, and Guiana Shield. The best-fit model identified the Guiana Shield as the likely ancestral area of the family, with dispersal events dominating over vicariance. Key areas for species interchange were the Amazon, Northern Andes, and Guiana Shield. The core regions of diversification included the Andes, Amazon, and Guiana Shield, with elevated species richness and biotic interchange events during the Eocene and Oligocene. The Guiana Shield stood out as a stronghold of gymnophthalmid diversity, driven by dispersal rates and ancient lineages. Our findings challenge previous hypotheses about the diversification of these lizards, suggesting a colonization pattern from lowlands to high elevations rather than the South-to-North Speciation Hypothesis for Andean lineages. [ABSTRACT FROM AUTHOR]

Pinnipeds (seals, sea lions, walruses, and their fossil relatives) are one of the most successful mammalian clades to live in the oceans. Despite a well-resolved molecular phylogeny and a global fossil record, a complete understanding of their macroevolutionary dynamics remains hampered by a lack of formal analyses that combine these 2 rich sources of information. We used a meta-analytic approach to infer the most densely sampled pinniped phylogeny to date (36 recent and 93 fossil taxa) and used phylogenetic paleobiological methods to study their diversification dynamics and biogeographic history. Pinnipeds mostly diversified at constant rates. Walruses, however, experienced rapid turnover in which extinction rates ultimately exceeded speciation rates from 12 to 6 Ma, possibly due to changing sea levels and/or competition with otariids (eared seals). Historical biogeographic analyses, including fossil data, allowed us to confidently identify the North Pacific and the North Atlantic (plus or minus Paratethys) as the ancestral ranges of Otarioidea (eared seals + walrus) and crown phocids (earless seals), respectively. Yet, despite the novel addition of stem pan-pinniped taxa, the region of origin for Pan-Pinnipedia remained ambiguous. These results suggest further avenues of study in pinnipeds and provide a framework for investigating other groups with substantial extinct and extant diversity. [ABSTRACT FROM AUTHOR]

Aim: Shifts in diversification rates of Australian flora and fauna have been associated with aridification, but the relationship between diversification rates and aridity has never been quantified. We employed multiple approaches to reconstruct paleoenvironments of Australia for the first time. We used this information, and phylogenetic‐based analyses, to explore how changes in temperature and increasing aridity during the Neogene influenced the diversification of the Australian blindsnakes. We tested whether diversification rates differ between arid‐adapted and mesic‐adapted lineages. Taxon: Typhlopidae, Anilios blindsnakes. Location: Australia. Materials and Methods: We estimated the historical biogeography of blindsnakes using BioGeoBEARS. We synthesised multiple approaches to reconstruct paleotemperature and paleoaridity of Australia during the Neogene. We fitted several birth‐death models and estimated diversification rates under paleoenvironmental conditions using RPANDA. We further compared diversification rates between arid‐adapted lineages versus mesic‐adapted lineages using ClaDS and GeoHiSSE. Results: Ancestral area estimation indicated Australian blindsnakes have tropical grassland origins. We found that Australia‐specific regional paleotemperature and paleoaridity provided a better explanation for diversification rate variation than global paleotemperature. Specifically, our best‐fitting model indicated that speciation rates of blindsnakes decreased with increasing aridity. We found no difference in diversification rates between arid‐ and mesic‐adapted lineages. Main Conclusions: Soon after dispersing to Australia, the common ancestors of Australian blindsnakes diversified rapidly in mesic habitats during the early Miocene. However, as the continent became increasingly arid, diversification rates decreased. We found that shifts in the environment led to the emergence of two major clades: one remaining in primarily mesic habitats and the other adapting to the expanding arid biome. Our results emphasise the importance of both arid and tropical biomes as sources and sinks of diversification. [ABSTRACT FROM AUTHOR]

Extant neosuchian crocodiles are represented by only 24 taxa that are confined to the tropics and subtropics. However, at other intervals during their 200 Myr evolutionary history the clade reached considerably higher levels of species-richness, matched by more widespread distributions. Neosuchians have occupied numerous habitats and niches, ranging from dwarf riverine forms to large marine predators. Despite numerous previous studies, several unsolved questions remain with respect to their biogeographic history, including the geographical origins of major groups, e.g. Eusuchia and Neosuchia itself. We carried out the most comprehensive biogeographic analysis of Neosuchia to date, based on a multivariate K-means clustering approach followed by the application of two ancestral area estimation methods (BioGeoBEARS and Bayesian ancestral location estimation) applied to two recently published phylogenies. Our results place the origin of Neosuchia in northwestern Pangaea, with subsequent radiations into Gondwana. Eusuchia probably emerged in the European archipelago during the Late Jurassic/Early Cretaceous, followed by dispersals to the North American and Asian landmasses. We show that putative transoceanic dispersal events are statistically significantly less likely to happen in alligatoroids. This finding is consistent with the saltwater intolerant physiology of extant alligatoroids, bolstering inferences of such intolerance in their ancestral lineages.

During the radiation of a clade, diversification rates can show temporal patterns such as a speedup or slowdown, which might relate to different ecological and evolutionary mechanisms. The temporal dynamics of diversification of whole clades are often visualised as a lineage-through-time (LTT) plot, which traces the number of reconstructed lineages at different time points. However, clades do not radiate evenly across space and may show different temporal dynamics in different regions. As such, a biogeographic approach is required to more completely understand temporal diversification dynamics. Here, I present a tool to extract temporal diversity information across different biogeographic regions from the output of commonly used ancestral range estimation models implemented in the R package BioGeoBEARS. The lineages through space and time (LTST) plot allows for visualisation of diversification dynamics in different regions, formatted in an accessible way which can be used for further quantitative analysis.

Nemognathinae is the most widespread subfamily of Meloidae, with ~600 species, and includes the only blister beetles distributed in Australia and on islands of the western Pacific. Four tribes are recognised based on morphology: Stenoderini, Palaestrini, Horiini and Nemognathini. Using two mitochondrial (16S , COI) and three nuclear markers (CAD , 28S , ITS2), and both maximum likelihood and Bayesian approaches, this study describes the evolutionary history of Nemognathinae based on molecular data for the first time. We provided a fossil-calibrated phylogeny that unravels the phylogenetic relationships among the tribes and among most of the genera, and a reconstruction of the biogeographic history using a parametric approach. Our results recognised the four tribes that were described previously based on morphology and revealed the presence of another well-differentiated clade corresponding to the genus Zoltanzonitis. Phylogenetic relationships among the tribes are well supported, with Stenoderini as the most ancient lineage, followed by Zoltanzonitini, Palaestrini, Horiini and Nemognathini. A few long-standing genera within Nemognathini (Nemognatha , Zonitis , Stenoria) and the nominate subgenus Stenodera (Stenodera) were recovered as polyphyletic. In addition, biogeographic analyses revealed the origin of the subfamily in the Old World during the Eocene, and the associated diversification into the five tribes astride the Eocene and Oligocene between 46 and 30 Ma. Based on these results we propose the new tribe Zoltanzonitini, and the elevation of the subgenus Pronemognatha to genus level, new status. In addition, Zonitoschema breveapicalis new comb. , Z. curticeps new comb. and Z. pulchella new status are proposed. ZooBank: urn:lsid:zoobank.org:pub:72EECC6D-36A6-4DD7-B4DB-D0692034E775. Nemognathinae is the most widespread Meloidae subfamily, with ~600 species, among which are the only blister beetle species that occur in Oceania. A comprehensive molecular phylogeny for the group is lacking. We investigated the history of this subfamily with a fossil-calibrated molecular approach, revealing the presence of a new tribe, the polyphyly of a few genera and an Eocene origin in the Old World. This work represents the first molecular phylogeny of Nemognathinae and contributes to revealing the evolutionary history of the Meloidae. [ABSTRACT FROM AUTHOR]

Aim: Statistical model comparison has become common in historical biogeography, enabled by the R package BioGeoBEARS, which implements several models in a common framework, allowing models to be compared with standard likelihood‐based methods of statistical model comparison. Ree and Sanmartín (Journal of Biogeography, 45, 741–749, 2018) critiqued the comparison of Dispersal–Extinction–Cladogenesis (DEC) and a modification of it, DEC+J, which adds the process of jump dispersal at speciation. DEC+J provides highly significant improvements in model fit on most (although not all) datasets. They claim that the comparison is statistically invalid for a variety of reasons. I analyse the key claims made by the critique. Location: Simulated data. Taxon: Simulated data. Methods: Likelihood calculations are checked by comparison between programs and by‐hand calculations, and by summing likelihoods across all possible datasets. Model adequacy of DEC versus DEC+J is checked by a simulation/inference experiment. Results: Mistakes in the critique's example likelihood calculations are demonstrated. DEC+J fits better on datasets because the DEC model is statistically inadequate in the common situation when most species have geographical ranges of single areas; the DEC model requires long residence times of multi‐area ranges, and when these are not observed, a model that does produce such data patterns, such as DEC+J, prevails. More fundamentally, statistical comparison of DEC and DEC+J produces identical log‐likelihood differences to statistical comparison of two submodels of ClaSSE where extinction rates are fixed to 0. Main Conclusions: DEC fails a basic model adequacy check for understandable reasons, while DEC+J does not. As Ree and Sanmartín recommend ClaSSE models as valid for comparison, the comparison of DEC and DEC+J is statistically valid according to their own criteria. [ABSTRACT FROM AUTHOR]

A detailed phylogeny of bumblebees is urgently needed to understand speciation and biogeographic diversification in the Neotropical region. We sequenced autosomal and mtDNA loci from nine Brazilian bumblebee species and compiled it with the data already available to obtain highly resolved phylogenetic trees with fossil-calibrated dates. The ancestral Bombus lineage was estimated to diversify between 47.08 and 34.27 million years ago (Ma) in the Holarctic region, but largely restricted to the eastern Old World. The Neotropical region was initially colonized in the Late Miocene, where bumblebee diversification was shown to be consistent with geologic and climatic events of the Late Cenozoic. Neotropical bumblebees likely originated from Nearctic lineages, which dispersed towards South America after 29 Ma. [ABSTRACT FROM AUTHOR]

Abstract Background The immense geologic and ecological complexity of the Caribbean has created a natural laboratory for interpreting when and how organisms disperse through time and space. However, competing hypotheses compounded with this complexity have resulted in a lack of unifying principles of biogeography for the region. Though new data concerning the timing of geologic events and dispersal events are emerging, powerful new analytical tools now allow for explicit hypothesis testing. Arthropods, with varying dispersal ability and high levels of endemism in the Caribbean, are an important, albeit understudied, biogeographic model system. Herein, we include a comprehensive analysis of every publicly available genetic dataset (at the time of writing) of terrestrial Caribbean arthropod groups using a statistically robust pipeline to explicitly test the current extent of biogeographic hypotheses for the region. Results Our findings indicate several important biogeographic generalizations for the region: the South American continent is the predominant origin of Caribbean arthropod fauna; GAARlandia played a role for some taxa in aiding dispersal from South America to the Greater Antilles; founder event dispersal explains the majority of dispersal events by terrestrial arthropods, and distance between landmasses is important for dispersal; most dispersal events occurred via island hopping; there is evidence of ‘reverse’ dispersal from islands to the mainland; dispersal across the present-day Isthmus of Panama generally occurred prior to 3 mya; the Greater Antilles harbor more lineage diversity than the Lesser Antilles, and the larger Greater Antilles typically have greater lineage diversity than the smaller islands; basal Caribbean taxa are primarily distributed in the Greater Antilles, the basal-most being from Cuba, and derived taxa are mostly distributed in the Lesser Antilles; Jamaican taxa are usually endemic and monophyletic. Conclusions Given the diversity and deep history of terrestrial arthropods, incongruence of biogeographic patterns is expected, but focusing on both similarities and differences among divergent taxa with disparate life histories emphasizes the importance of particular qualities responsible for resulting diversification patterns. Furthermore, this study provides an analytical toolkit that can be used to guide researchers interested in answering questions pertaining to Caribbean biogeography using explicit hypothesis testing.

Allioideae (e.g., chives, garlics, onions) comprises three mainly temperate tribes: Allieae (800 species from the northern hemisphere), Gilliesieae (80 South American species), and Tulbaghieae (26 Southern African species). We reconstructed the phylogeny of Allioideae (190 species plus 257 species from Agapanthoideae and Amaryllidoideae) based on ITS, matK, ndhF, and rbcL to investigate its historical biogeography and karyotype evolution using newly generated cytomolecular data for Chilean Gilliesieae genera Gethyum, Miersia, Solaria, and Speea. The crown group of Allioideae diversified ∼62 Mya supporting a Gondwanic origin for the subfamily and vicariance as the cause of the intercontinental disjunction of the tribes. Our results support the hypothesis of the Indian tectonic plate carrying Allieae to northern hemisphere (‘out-of-India’ hypothesis). The colonization of the northern hemisphere (∼30 Mya) is correlated with a higher diversification rate in Allium associated to stable x = 8, increase of polyploidy and the geographic expansion in Europe and North America. Tulbaghieae presented x = 6, but with numerical stability (2n = 12). In contrast, the tribe Gilliesieae (x = 6) varied considerably in genome size (associated with Robertsonian translocations), rDNA sites distribution and chromosome number. Our data indicate that evolutionary history of Allioideae tribes is linked to distinct trends of karyotype evolution.

The Andes is recognized as one of the most biodiverse places on Earth, promoting in its uplift process a series of recent rapid diversification events in different biotic groups like birds, mammals, insects and vascular plants. The uplift of the Andes during the Cenozoic acted as a barrier for many biotic groups, as a scenario for radiation processes due to occupancy of different niches and as a corridor for others. Connections between the Andes and the Atlantic Forest showed intermittent phases along the Cenozoic, affecting the distribution patterns and diversification of different biotic groups. Nowadays, the Andes and the Atlantic Forest are both considered globally relevant biodiversity hotspots. Floristic groups thriving in both hotspots are crucial for a better understanding of their biogeographic history, as well as for informing future conservation actions. Mutisia (Asteraceae), a genus comprising 63 perennial shrubs and vines endemic to South America, shows a marked West-East disjunction: Most species occupy almost the whole Andean chain from Colombia to Patagonia, while a second group encompasses four species distributed in eastern Brazil and the surrounding areas of Paraguay, Uruguay and Argentina. We reconstructed the phylogeny of the genus to assess its possible biogeographic history. We analysed three DNA regions, i.e. the chloroplast trnL-trnF intergenic spacer and the nuclear ribosomal internal and external transcribed spacers, ITS and ETS. Using maximum likelihood and Bayesian inference, gene trees were reconstructed, and a concatenated phylogenetic tree was inferred. Divergence times were estimated by means of BEAST, and the ancestral areas were inferred using BioGeoBEARS. An ancestral reconstruction of morphological traits was also performed, as well as maps representing current richness hotspots within the genus. Phylogenetic analyses strongly support the monophyly of Mutisia, with two well-supported main clades: clade A, with presence of Atlantic-central-northern Andes species, and clade B, with central/southern Andes species. Dating analyses suggest that a main clade separation occurred at the early Miocene, followed by the separation of the Atlantic clade A2 by the late Miocene, and more recent radiations occurred in the central, northern and southern Andes during the Pliocene. Results are in tune with other angiosperm taxa that also underwent rapid radiations, possibly related to environmental and pollinator changes. The biogeographic history of Mutisia is related to morphological adaptations, history and geographic factors acting since the Miocene along the Andes and adjacent areas. Threat assessments and conservation actions for the genus shall include the whole distribution range, including low-range northern and southern Andes species, as well as the distinctive Atlantic Forest clade. [ABSTRACT FROM AUTHOR]

Allioideae (e.g., chives, garlics, onions) comprises three mainly temperate tribes: Allieae (800 species from the northern hemisphere), Gilliesieae (80 South American species), and Tulbaghieae (26 Southern African species). We reconstructed the phylogeny of Allioideae (190 species plus 257 species from Agapanthoideae and Amaryllidoideae) based on ITS, mat K, ndh F, and rbc L to investigate its historical biogeography and karyotype evolution using newly generated cytomolecular data for Chilean Gilliesieae genera Gethyum , Miersia , Solaria , and Speea. The crown group of Allioideae diversified ∼62 Mya supporting a Gondwanic origin for the subfamily and vicariance as the cause of the intercontinental disjunction of the tribes. Our results support the hypothesis of the Indian tectonic plate carrying Allieae to northern hemisphere ('out-of-India' hypothesis). The colonization of the northern hemisphere (∼30 Mya) is correlated with a higher diversification rate in Allium associated to stable x = 8, increase of polyploidy and the geographic expansion in Europe and North America. Tulbaghieae presented x = 6, but with numerical stability (2 n = 12). In contrast, the tribe Gilliesieae (x = 6) varied considerably in genome size (associated with Robertsonian translocations), rDNA sites distribution and chromosome number. Our data indicate that evolutionary history of Allioideae tribes is linked to distinct trends of karyotype evolution. [ABSTRACT FROM AUTHOR]

Background: The immense geologic and ecological complexity of the Caribbean has created a natural laboratory for interpreting when and how organisms disperse through time and space. However, competing hypotheses compounded with this complexity have resulted in a lack of unifying principles of biogeography for the region. Though new data concerning the timing of geologic events and dispersal events are emerging, powerful new analytical tools now allow for explicit hypothesis testing. Arthropods, with varying dispersal ability and high levels of endemism in the Caribbean, are an important, albeit understudied, biogeographic model system. Herein, we include a comprehensive analysis of every publicly available genetic dataset (at the time of writing) of terrestrial Caribbean arthropod groups using a statistically robust pipeline to explicitly test the current extent of biogeographic hypotheses for the region. Results: Our findings indicate several important biogeographic generalizations for the region: the South American continent is the predominant origin of Caribbean arthropod fauna; GAARlandia played a role for some taxa in aiding dispersal from South America to the Greater Antilles; founder event dispersal explains the majority of dispersal events by terrestrial arthropods, and distance between landmasses is important for dispersal; most dispersal events occurred via island hopping; there is evidence of 'reverse' dispersal from islands to the mainland; dispersal across the present-day Isthmus of Panama generally occurred prior to 3 mya; the Greater Antilles harbor more lineage diversity than the Lesser Antilles, and the larger Greater Antilles typically have greater lineage diversity than the smaller islands; basal Caribbean taxa are primarily distributed in the Greater Antilles, the basal-most being from Cuba, and derived taxa are mostly distributed in the Lesser Antilles; Jamaican taxa are usually endemic and monophyletic. Conclusions: Given the diversity and deep history of terrestrial arthropods, incongruence of biogeographic patterns is expected, but focusing on both similarities and differences among divergent taxa with disparate life histories emphasizes the importance of particular qualities responsible for resulting diversification patterns. Furthermore, this study provides an analytical toolkit that can be used to guide researchers interested in answering questions pertaining to Caribbean biogeography using explicit hypothesis testing. [ABSTRACT FROM AUTHOR]

Aim: Almost half of the extant species of Crocodylia (nine genera, sensu Benton & Clark) belong to the genus Crocodylus, which originated in the Miocene. Today, this genus has a circumtropical distribution, with representatives found in Asia, Oceania, Africa and the Neotropics. However, its geographical origin and the historical events behind its rapid diversification and global radiation are still debated. Here, we inferred the evolution of a set of life traits that aid in dispersal and how they influenced the biogeography of Crocodylus. Location: Global. Time period: Cretaceous to the present. Major taxa studied: Crocodylidae. Methods: We estimated biogeographical history on a published phylogeny using probabilistic biogeography models. Next, we identified four life traits likely to promote range expansion and used a trait‐based dispersal model jointly to infer evolution of these traits and their influence on the dispersal of crocodilians. Finally, we used diversification analyses to identify shifts in diversification rates. Results: An Asian origin was reconstructed for Crocodylus. Despite the small size of the phylogeny, statistical model comparison reports substantially improved the model fit of trait‐dependent over trait‐independent dispersal models. In individual tests, the four life traits considered (salt tolerance, large size, large clutches and habitat generalism) appear to be correlated statistically with higher dispersal probabilities. However, the traits are likely to be correlated with each other, and we hypothesize that they all reflect the gradual evolution of a range‐expansion phenotype in early Crocodylus that resulted in increased diversification of the clade. Main conclusions: Increased dispersal in the genus Crocodylus was associated with the gradual evolution of a range‐expansion phenotype. Interestingly, the evolution of the range‐expansion phenotype was also associated with the diversification of the genus in a period of global crocodilian extinction, indicating that range expansion might have served as a potential driver of speciation. This suggests that the concept of "spatial sorting", normally applied at the population genetic level at the leading edge of an expanding population, might also act on a macroevolutionary scale. [ABSTRACT FROM AUTHOR]

• The subfamily Rimulinae is recognized for Rimula , sister group to all other fissurellids. • Many emarginuline genera are recovered in Zeidorinae (previously Hemitominae). • Emarginula , Diodora , Fissurella are not monophyletic and need systematic revision. • Crown fissurellids originated ca. 175 Ma in the Tethys Sea curr. Indo-West Pacific. • The Atlantic was colonized via the Tethys Seaway, serving as source for further dispersal. Fissurellidae are marine gastropods with a worldwide distribution and a rich fossil record. We integrate molecular, geographical and fossil data to reconstruct the fissurellid phylogeny, estimate divergence times and investigate historical routes of oceanic dispersal. With five molecular markers for 143 terminals representing 27 genera, we resolve deep nodes and find that many genera (e.g., Emarginula , Diodora , Fissurella) are not monophyletic and need systematic revision. Several genera classified as Emarginulinae are recovered in Zeidorinae. Future work should prioritize emarginuline genera to improve understanding of ancestral traits and the early evolution of fissurellids. Tree calibration with the fossilized birth-death model indicates that crown fissurellids originated around 175 Ma, and generally resulted in younger ages for the earliest nodes than the node dating approach. Model-based biogeographic reconstruction, supported by fossils, infers an Indo-West Pacific origin, with a westward colonization of new oceans via the Tethys Seaway upon the breakup of Pangea. Western Atlantic clades then served as source for dispersal towards other parts of the globe. As the sister group to all other fissurellids, Rimula is ranked in its own subfamily, Rimulinae stat. nov. New synonyms: Hemitominae syn. nov. of Zeidorinae stat. nov. ; Cranopsis syn. nov. of Puncturella ; Variegemarginula syn. nov. of Montfortula. [ABSTRACT FROM AUTHOR]

Dinosaurs were ubiquitous in terrestrial ecosystems through most of the Mesozoic and are still diversely represented in the modern fauna in the form of birds. Recent efforts to better understand the origins of the group have resulted in the discovery of many new species of early dinosaur and their closest relatives (dinosauromorphs). In addition, recent re‐examinations of early dinosaur phylogeny have highlighted uncertainties regarding the interrelationships of the main dinosaur lineages (Sauropodomorpha, Theropoda and Ornithischia), and questioned the traditional hypothesis that the group originated in South Gondwana and gradually dispersed over Pangaea. Here, we use an historical approach to examine the impact of new fossil discoveries and changing phylogenetic hypotheses on biogeographical scenarios for dinosaur origins over 20 years of research time, and analyse the results in the light of different fossil record sampling regimes. Our results consistently optimize South Gondwana as the ancestral area for Dinosauria, as well as for more inclusive clades including Dinosauromorpha, and show that this hypothesis is robust to increased taxonomic and geographic sampling and divergent phylogenetic results. Our results do not find any support for the recently proposed Laurasian origin of dinosaurs and suggest that a southern Gondwanan origin is by far the most plausible given our current knowledge of the diversity of early dinosaurs and non‐dinosaurian dinosauromorphs. [ABSTRACT FROM AUTHOR]

The Late Jurassic Tendaguru Formation of Tanzania, southeastern Africa, records a rich sauropod fauna, including the diplodocoids Dicraeosaurus and Tornieria, and the brachiosaurid titanosauriform Giraffatitan. However, the taxonomic affinities of other sympatric sauropod taxa are poorly understood. Here, we critically reassess and redescribe these problematic taxa, and present the largest phylogenetic analysis for sauropods (117 taxa scored for 542 characters) to explore their placement in Eusauropoda. Janenschia robusta has played a prominent role in discussions of titanosaur origins, with various authors referring at least some remains to Titanosauria, a clade otherwise known only from the Cretaceous. Redescription of the holotype of Janenschia, and all referable remains, supports its validity and placement as a non-neosauropod eusauropod. It forms a clade with Haestasaurus from the earliest Cretaceous of the UK, and the Middle/Late Jurassic Chinese sauropod Bellusaurus. Phylogenetic analysis and CT scans of the internal pneumatic tissue structure of Australodocus bohetii tentatively support a non-titanosaurian somphospondylan identification, making it the only known pre-Cretaceous representative of that clade. New information on the internal pneumatic tissue structure of the dorsal vertebrae of the enigmatic Tendaguria tanzaniensis, coupled with a full redescription, results in its novel placement as a turiasaur. Tendaguria is the sister taxon of Moabosaurus, from the Early Cretaceous of North America, and is the first turiasaur recognized from Gondwana. A previously referred caudal sequence cannot be assigned to Janenschia and displays several features that indicate a close relationship with Middle–Late Jurassic East Asian mamenchisaurids. It can be diagnosed by six autapomorphies, so we erect the new taxon Wamweracaudia keranjei gen. et sp. nov. The presence of a mamenchisaurid in the Late Jurassic of southern Gondwana indicates an earlier and more widespread diversification of this clade than previously realized, prior to the geographic isolation of East Asia. Our revised phylogenetic dataset sheds light on the evolutionary history of Eusauropoda, including supporting a basal diplodocoid placement for Haplocanthosaurus, and elucidating the interrelationships of rebbachisaurids. The Tendaguru Formation shares representatives of nearly all sauropod lineages with Middle Jurassic–earliest Cretaceous global faunas, but displays a greater range of diversity than any of those faunas considered individually. Biogeographic analysis indicates that the Tendaguru sauropod fauna was assembled as a result of three main phenomena during the late Early and/or Middle Jurassic: (1) invasions from Euramerica (brachiosaurids, turiasaurs); (2) endemism in west Gondwana (dicraeosaurids, diplodocids); and (3) regional extinctions that restricted the ranges of once widespread groups (mamenchisaurids, the Janenschia lineage). Multiple dispersals across the Central Gondwanan Desert are required to explain the distributions of Jurassic sauropods, suggesting that this geographic feature was at most a filter barrier that became easier to cross during the late Middle Jurassic. [ABSTRACT FROM AUTHOR]

Peat mosses (Sphagnum) hold exceptional importance in the control of global carbon fluxes and climate because of the vast stores of carbon bound up in partially decomposed biomass (peat). This study tests the hypothesis that the early diversification of Sphagnum was in the Northern Hemisphere, with subsequent range expansions to tropical latitudes and the Southern Hemisphere. A phylogenetic analysis of 192 accessions representing the moss class Sphagnopsida based on four plastid loci was conducted in conjunction with biogeographic analyses using BioGeoBEARS to investigate the tempo and mode of geographic range evolution. Analyses support the hypothesis that the major intrageneric clades of peat‐forming species accounting for >90% of peat moss diversity originated and diversified at northern latitudes. The genus underwent multiple range expansions into tropical and Southern Hemisphere regions. Range evolution in peat mosses was most common within latitudinal zones, attesting to the relative difficulty of successfully invading new climate zones. Allopolyploidy in Sphagnum (inferred from microsatellite heterozygosity) does not appear to be biased with regard to geographic region nor intrageneric clade. The inference that Sphagnum diversified in cool‐or cold‐climate regions and repeatedly expanded its range into tropical regions makes the genus an excellent model for studying morphological, physiological, and genomic traits associated with adaptation to warming climates. This study tests the hypothesis that Sphagnum (peat mosses) initially diversified at high latitudes of the Northern Hemisphere and later extended their ranges to tropical and Southern Hemisphere regions. The ancestral geographic area for the genus as a whole is ambiguous, but the four major subgenera, comprising some 90% of the generic species diversity, unambiguously originated at high latitudes. Sphagnum provides a model for research on genomic, ecological, and morphological changes associated with adaptation to warm climates from cold or cool climate ancestors. [ABSTRACT FROM AUTHOR]

Abstract: Titi monkeys, subfamily Callicebinae, are a diverse, species‐rich group of Neotropical primates with an extensive range across South America. Their distribution in space and time makes them an interesting primate model for addressing questions of Neotropical historical biogeography. Our aim was to reconstruct the biogeographic history of Callicebinae to better understand their diversification patterns and the history of their colonisation of South America since the late Miocene. We reconstructed a time‐calibrated phylogeny of 19 titi species under Bayesian inference using two mitochondrial and 11 nuclear loci. Species were assigned across eight Neotropical areas of endemism, and statistical biogeographic methods implemented in BioGeoBEARS were employed to estimate ancestral areas using 12 biogeographic models. Our results indicate that the most recent common ancestor to extant titi monkeys was widespread from the present‐day Andean foothills in the Colombian Amazon, through the wet and dry savannas of Bolivia and Brazil, to the southern Atlantic forest of eastern Brazil. Genus‐level divergences were characterised by vicariance of ancestral range in the late Miocene. Species‐level diversification in Cheracebus and the Plecturocebus moloch group occurred as they spread across the Amazon in the Pleistocene and were largely characterised by a sequential, long‐distance “island‐hopping” dispersal model of speciation from a narrow area of origin through jump dispersal across rivers. This study comprises the first large‐scale investigation of the evolutionary history of titi monkeys in the context of Amazonian and South American historical biogeography and sheds light on the processes that generated the great diversity found among Callicebinae. [ABSTRACT FROM AUTHOR]

The ‘out of Australia’ hypothesis describes taxa with ancestors present on the Australian continent before the contact of the Australian plate with Southeast Asia and the subsequent biological interchange between these regions across Wallacea. Our study supports the ‘out of Australia’ hypothesis for the tropical tree genus Alphitonia and its closest relatives. A common ancestor of the entire clade inhabited Australia in the Miocene, and westward dispersal into Wallacea, the Philippines and the Asian continent was reconstructed to be of Quaternary origin. Furthermore, our study supports the currently applied taxonomy in Alphitonia and related genera, although it highlights potentially underestimated diversity. Finally, our study highlights the need for further investigations in Alphitonia and related genera and for including fossil-rich related taxa. The need for these investigations also arises from a potential human-mediated dispersal of Alphitonia spp. in Polynesia, which cannot be clearly proven by our approach. [ABSTRACT FROM AUTHOR]

Darwin's finches are considered a classic example of an adaptive radiation, and have been the focus of numerous studies from ecological and evolutionary perspectives. Few studies, however, have attempted to investigate the biogeographic origins of Darwin's finches. In this paper, we reconstruct the ancestral biogeography of Coerebinae, the tanager subfamily that contains Darwin's finches and their 14 closest relatives. We use this reconstruction to examine the origin of Darwin's finches, and the diversification of this clade of tanagers. We test multiple biogeographic models using the R package BioGeoBEARS utilizing a recent multilocus phylogeny. We used these models to examine 2 different hypotheses regarding the biogeographic origin of Darwin's finches. The majority of ancestral ranges within this subfamily were estimated as Caribbean restricted. Biogeographic models run using 8 regions suggest Darwin's finches arose from a long-distance dispersal event from the Caribbean Islands as opposed to the geographically closer mainland South America. However, models run using only 5 areas suggest equal probability between a Caribbean and a mainland South America origin to Darwin's finches. This study suggests equal probability for a Caribbean origin to Darwin's finches as a South American mainland origin. Conflict between models run using different biogeographic regimes highlights the sensitivity of these reconstructions to biogeographic region delineation. Overall, the Caribbean Islands appear especially important for the initial diversification of this clade, with many small-island restricted species diversifying early in the radiation. Colonization success was likely coupled with high dispersal ability and highly variable bill morphology to exploit vacant niche space. [ABSTRACT FROM AUTHOR]

The family Margaritiferidae encompasses 12 valid species, which are distributed widely but disjunctively in the Northern Hemisphere. A lack of a well resolved and temporally calibrated phylogenetic framework of Margaritiferidae has made it difficult to discuss the evolutionary pattern and process. Phylogenetic relationships between five major clades, which were revealed in earlier studies, remain elusive and unresolved. Lamprotula rochechouartii has long been classified within the family Unionidae based on shell morphology, but our preliminary molecular study on this species made us hypothesize that it has an affinity with margaritiferids. Hence, five loci (COI, 16S, 18S, 28S and histone H3) were used to investigate the phylogenetic position of L. rochechouartii and intra-familial relationships within Margaritiferidae using various partitioning strategies. Moreover, two mitochondrial genomes were newly obtained to further resolve and validate the five-clade relationships within Margaritiferidae in a broad view of Unionoida evolution. Both five-gene and mitogenome datasets strongly advocated treating Lamprotula rochechouartii as Margaritifera rochechouartii comb . nov . Maximum likelihood and Bayesian inference analyses using partitioned five-gene dataset resulted in various topologies, but five well-supported clades were obtained. The most probable cladistic relationships generated by five-gene dataset analyses were identical to subsequent whole mitogenome analyses except the position of M. monodonta . M. rochechouartii and M. laosensis had a well-supported sister relationship and formed a basal clade splitting from the rest of the family. Based on six reliable fossils, crown age of the extant Margaritiferidae was estimated during the Late Cretaceous at 88.3 Ma (95% HPD = 66.2–117.4). But we hypothesized a much earlier origin of this family due to the Permian stem age (mean = 257 Ma, 95% HPD = 230.0–296.0) and a high extinction rate in the whole order. Biogeographic scenarios supported a Laurasian origin of extant Margaritiferidae during the Late Cretaceous, and suggested that Asian margaritiferids may have had two origins, having either Asia ( M. rochechouartii, M. laosensis ) or North America ( M. dahurica, M. laevis, and M. middendorffi ) as ancestral. The newly added Margaritiferidae species M. rochechouartii expands our recognized distribution range of modern margaritiferids. Our results indicate that whole mitogenome sequences can be used to reconstruct robust phylogenetic relationships for freshwater mussels, especially with the help of adding M-type mitogenomes. [ABSTRACT FROM AUTHOR]

Mexican dry environments are widespread and characterized by a rich flora and fauna in terms of both overall species diversity and endemism, but the factors that have shaped this diversity remain unclear. In this study, we evaluated hypotheses concerning the biogeographical origin and evolutionary history of Florestina (Asteraceae) in Mexican dry environments. For this, we generated a time-calibrated phylogenetic tree from the nuclear non-coding external and and internal transcribed spacers (ETS, ITS), using the program BEAST. Based on this phylogenetic tree, we employed the package BioGeoBEARS to infer the historical biogeography of the genus, comparing different biogeographical models and estimating the ancestral range probabilities. Our time-calibrated phylogenetic tree suggested that the genus Florestina diverged during the early Pliocene c. 5.2 Mya and diversification continued throughout the Pleistocene. Furthermore, results suggest that the biogeographical origin of the Hymenothrix/Palafoxia/Florestina clade was in Nearctic regions, not in Neotropical regions as previously suggested. We hypothesize that the ancestor of Florestina became disjunct and isolated in tropical dry forests of southern Mexico from Palafoxia after the rifting of the Baja California peninsula from the Mexican mainland. [ABSTRACT FROM AUTHOR]

PREMISE OF THE STUDY: The subtribe Menthinae (Lamiaceae), with 35 genera and 750 species, is among the largest and most economically important subtribes within the mint family. Most genera of Menthinae are found exclusively in the New World, where the group has a virtually continuous distribution ranging from temperate North America to southern South America. In this study, we explored the presence, timing, and origin of amphitropical disjuncts within Menthinae. METHODS: Our analyses were based on a data set consisting of 89 taxa and the nuclear ribosomal DNA markers ITS and ETS. Phylogenetic relationships were determined under maximum likelihood and Bayesian criteria, divergence times were estimated with the program BEAST, and ancestral range estimated with BioGeoBEARS. KEY RESULTS: A North Atlantic Land Bridge migration event at about 10.6 Ma is inferred from western Eurasia to North America. New World Menthinae spread rapidly across North America, and then into Central and South America. Several of the large speciose genera are not monophyletic with nuclear rDNA, a finding mirrored with previous chloroplast DNA results. Three amphitropical disjunctions involving North and southern South America clades, one including a southeastern South American clade with several genera, were inferred to have occurred within the past 5 Myr. CONCLUSIONS: Although three New World Menthinae genera occur in both North and South America, none exhibit an amphitropical disjunction. However, three clades exhibit amphitropical disjunctions, all dating to the early Pliocene, and all involve jump dispersals to either southeastern or southwestern South America from southeastern North America. [ABSTRACT FROM AUTHOR]

Despite their complex evolutionary history and the rich fossil record, the higher level phylogeny and historical biogeography of living turtles have not been investigated in a comprehensive and statistical framework. To tackle these issues, we assembled a large molecular dataset, maximizing both taxonomic and gene sampling. As different models provide alternative biogeographical scenarios, we have explicitly tested such hypotheses in order to reconstruct a robust biogeographical history of Testudines. We scanned publicly available databases for nucleotide sequences and composed a dataset comprising 13 loci for 294 living species of Testudines, which accounts for all living genera and 85% of their extant species diversity. Phylogenetic relationships and species divergence times were estimated using a thorough evaluation of fossil information as calibration priors. We then carried out the analysis of historical biogeography of Testudines in a fully statistical framework. Our study recovered the first large-scale phylogeny of turtles with well-supported relationships following the topology proposed by phylogenomic works. Our dating result consistently indicated that the origin of the main clades, Pleurodira and Cryptodira, occurred in the early Jurassic. The phylogenetic and historical biogeographical inferences permitted us to clarify how geological events affected the evolutionary dynamics of crown turtles. For instance, our analyses support the hypothesis that the breakup of Pangaea would have driven the divergence between the cryptodiran and pleurodiran lineages. The reticulated pattern in the ancestral distribution of the cryptodiran lineage suggests a complex biogeographic history for the clade, which was supposedly related to the complex paleogeographic history of Laurasia. On the other hand, the biogeographical history of Pleurodira indicated a tight correlation with the paleogeography of the Gondwanan landmasses. [ABSTRACT FROM AUTHOR]

Aim Our aim was to examine gracile capuchin ( Cebus) and robust capuchin monkey ( Sapajus) diversification, with a focus on recent Sapajus expansion within Amazonia. We wanted to reconstruct the biogeographical history of the clade using statistical methods that model lineages' occupation of different regions over time in order to evaluate recently proposed 'Out of Amazonia' and 'Reinvasion of Amazonia' hypotheses as alternative explanations for the extensive geographical overlap between reciprocally monophyletic gracile ( Cebus) and robust ( Sapajus) capuchin monkeys. Location Central and South America. Methods We reconstructed a time-calibrated molecular phylogeny for capuchins under Bayesian inference from three mitochondrial genes. We then categorized 12 capuchin clades across four Neotropical centres of endemism and reconstructed the biogeographical history of the capuchin radiation using six models implemented in 'BioGeo BEARS'. We performed a phylogeographical analysis for a robust capuchin clade that spans the Atlantic Forest, Cerrado, Caatinga and Amazonia. Results We find support for a late Miocene vicariant Cebus-Sapajus divergence and a Pleistocene Sapajus invasion of Amazonia from the Atlantic Forest. Our new analyses confirm Sapajus diversified first in the Atlantic Forest, with subsequent range expansion into widespread sympatry with Cebus in Amazonia, as well as multiple expansions into drier savanna-like habitats. We do not find mitochondrial molecular congruence with morphological species distinctions for Sapajus flavius, S. cay, S. macrocephalus, S. libidinosus and S. apella; instead, these five morphological types together form a single widespread clade (Bayesian posterior probability = 1) with geographical substructure and shared ancestry during the Pleistocene. Main conclusions Our results support vicariance dividing ancestral capuchin populations in Amazonia versus the Atlantic Forest, and a Pleistocene 'Amazonian invasion' by Sapajus to explain the present-day sympatry of Cebus and Sapajus. [ABSTRACT FROM AUTHOR]

Aim The tomato family Solanaceae is distributed on all major continents except Antarctica and has its centre of diversity in South America. Its worldwide distribution suggests multiple long-distance dispersals within and between the New and Old Worlds. Here, we apply maximum likelihood ( ML) methods and newly developed biogeographical stochastic mapping ( BSM) to infer the ancestral range of the family and to estimate the frequency of dispersal and vicariance events resulting in its present-day distribution. Location Worldwide. Methods Building on a recently inferred megaphylogeny of Solanaceae, we conducted ML model fitting of a range of biogeographical models with the program 'BioGeo BEARS'. We used the parameters from the best fitting model to estimate ancestral range probabilities and conduct stochastic mapping, from which we estimated the number and type of biogeographical events. Results Our best model supported South America as the ancestral area for the Solanaceae and its major clades. The BSM analyses showed that dispersal events, particularly range expansions, are the principal mode by which members of the family have spread beyond South America. Main conclusions For Solanaceae, South America is not only the family's current centre of diversity but also its ancestral range, and dispersal was the principal driver of range evolution. The most common dispersal patterns involved range expansions from South America into North and Central America, while dispersal in the reverse direction was less common. This directionality may be due to the early build-up of species richness in South America, resulting in large pool of potential migrants. These results demonstrate the utility of BSM not only for estimating ancestral ranges but also in inferring the frequency, direction and timing of biogeographical events in a statistically rigorous framework. [ABSTRACT FROM AUTHOR]

Subsequent to the Miocene (approximately 35 Mya), Borneo has served as an insular refuge and a source of colonization for a broad range of species emigrating to others parts of Sundaland. A phylogeny-based historical biogeographical hypothesis for the Stream Toad genus Ansonia supports multiple instances of an out-of-Borneo scenario. An ancestral range estimation indicates that in situ speciation of Ansonia on the island of Borneo during the Late Miocene and Pliocene (approximately 2-13 Mya) eventually resulted in an invasion of the Philippines, Sumatra, and two independent invasions of the Thai-Malay Peninsula. When collecting material for the biogeographical analysis, a new species of Ansonia, Ansonia khaochangensis sp. nov. was discovered in a limestone cave from the Khao Chang karst tower in Phangnga Province, in southern Thailand. Ansonia khaochangensis sp. nov. can be differentiated from all other species of Ansonia by having a unique combination of morphological and colour pattern characteristics. Phylogenetic evidence based on the mitochondrial genes 12S and 16S indicates that it is nested within a clade of other species distributed north of the Isthmus of Kra. The cave lifestyle of this new species is a unique and a significant departure from lotic environments common to most other species of Ansonia. The reproductive biology of this species is unknown. [ABSTRACT FROM AUTHOR]

Aim: A prevailing hypothesis for how Pacific islands organisms have obtained their extant distributions is that of a stepping-stone model, in which populations originate from Papua New Guinea in the western Pacific and gradually disperse eastward. Here, we test this model using a spatiotemporal framework for Emoia cyanura and E. impar, two species within the Emoia cyanura species group (ECSG; Family: Scincidae). We further assess species limits within the group, utilizing novel coalescent methods. Location: Pacific Islands. Methods: We obtained DNA sequence data from one mitochondrial and three nuclear markers for 117 individuals, representing seven of the nine species within the ECSG. These data were analysed for concordance with the steppingstone model using estimation of population structure, divergence dates, and historical biogeographical range. To assess hypotheses of independent lineages within each widespread species, we also employed the Bayesian Phylogenetics & Phylogeography (BPP) program to define operational taxonomic units in *BEAST. Results: Population structure analyses consistently found individuals from western island groups representing divergent populations, with central and eastern populations demonstrating minimal genetic variation. Phylogenetic hypotheses support a western origin for E. cyanura and E. impar, while biogeographical and divergence time estimations predict a recent and rapid expansion out of the western Pacific. The BPP and *BEAST analyses found evidence for five independent lineages within E. impar and five independent lineages within E. cyanura/E. pseudocyanura. Main conclusions: In contrast to the expectations of a stepping-stone model, E. cyanura and E. impar each exhibit the genetic signature of a rapid radiation during the mid to late Pleistocene, with evidence for newly identified lineages, mainly on western islands. Of these recovered lineages, we propose three to be elevated to species status. These findings expand our understanding of endemic Pacific biota, which are subject to conservation threats from human impacts and climate change. [ABSTRACT FROM AUTHOR]

Aim: Here, I investigate galagid diversification and current distribution in the context of major climatic and geological events in sub-Saharan Africa. Given their widespread distribution and presence in a large range of diverse habitats, galagids represent an excellent group to investigate the role of forest contraction and expansion on biological diversification in sub-Saharan Africa. Location: Sub-Saharan Africa (Afrotropical Region). Methods: I assembled a supermatrix including 53 nuclear loci and three mitochondrial markers for 94% of the galagid species currently recognized. Bayesian and maximum likelihood methods were used to infer phylogenetic relationships and times of divergence within the family. Ancestral ranges were estimated using several methods, including 'BioGeoBEARS' and rasp. Results: Phylogenetic analyses corroborated previous results regarding the evolutionary history of this family: (1) early origin of the family soon after the Eocene-Oligocene boundary; (2) dwarf galagos (Galagoides spp.) represent a polyphyletic group with two well-defined clades, one in central-west Africa and one in the east; and (3) divergences within galagids are relatively old with most genera already present by the Late Miocene. The biogeographical analysis indicates central African origins and subsequent expansion to the east in the Early- Middle Miocene. An expansion to the northern and southern savannas occurred between the Late Pliocene and the Middle Pleistocene. Main conclusions: The results of this study clarify several questions related to the evolutionary history of the Galagidae in the context of sub-Saharan African biogeography. This study suggests that galagid evolution and diversification was affected by three major climatic episodes: (1) the global cooling and forest contraction in the Early Oligocene, (2) the forest expansion and the uplift of the African rifts in the Miocene and (3) the aridification and extension of open woodlands and savannas in the Late Miocene and Plio-Pleistocene. [ABSTRACT FROM AUTHOR]

Aim: Orchidaceae is the most species-rich angiosperm family and has one of the broadest distributions. Until now, the lack of a well-resolved phylogeny has prevented analyses of orchid historical biogeography. In this study, we use such a phylogeny to estimate the geographical spread of orchids, evaluate the importance of different regions in their diversification and assess the role of long-distance dispersal (LDD) in generating orchid diversity. Location: Global. Methods: Analyses use a phylogeny including species representing all five orchid subfamilies and almost all tribes and subtribes, calibrated against 17 angiosperm fossils. We estimated historical biogeography and assessed the importance of different regions for rates of speciation, extinction and net species diversification. We evaluated the impact of particular LDD events on orchid diversity by asking how many species evolved in the new range subsequent to those events. Results: Orchids appear to have arisen in Australia 112 Ma (95% higher probability distribution: 102.0-120.0 Ma), then spread to the Neotropics via Antarctica by 90 Ma (HPD: 79.7-99.5 Ma), when all three continents were in close contact and apostasioids split from the ancestor of all other orchids. Ancestors of vanilloids, cypripedioids and orchidoids+epidendroids appear to have originated in the Neotropics 84-64 Ma. Repeated long- and short-distance dispersal occurred through orchid history: stochastic mapping identified a mean total of 74 LDD events or 0.8 Ma-1. Across orchid history, Southeast Asia was the most important source and maximally accelerated net diversification; across epidendroids, the Neotropics maximally accelerated diversification. Main conclusions: Our analysis provides the first biogeographical history of the orchids, implicating Australia, the Neotropics and Antarctica in their origin. LDD and life in the Neotropics - especially the Andes - had profound effects on their spread and diversification; > 97% of all orchid species are restricted to individual continents. [ABSTRACT FROM AUTHOR]

Aim: Across angiosperm families, the area occupied by a family is strongly correlated with its richness. We explore the causes of this area-richness correlation using the cosmopolitan family, Cyperaceae Juss., as a model. We test the hypothesis that, despite a proposed tropical origin, temperate lineages in the family diversified at elevated rates. We test the hypothesis that the area-richness correlation is maintained within intrafamilial clades, and that this relationship could be described as a function of niche space. We also test the hypothesis that the partitioning of geographical and ecological space, not the extent of this space, is the factor most closely associated with clade richness. Location: Cosmopolitan. Methods: We use molecular data from four genes sequenced in 384 taxa to develop a chronogram of Cyperaceae. We then develop a model of ancestral ranges and measure rates of diversification throughout the history of the family. Integrating data from over 4,800,000 digitized herbarium records, we characterize the range and niche of more than 4500 species and test for correlations of the species richness maintained within clades with range size, range partitioning, range overlap, niche, clade age and rate of diversification. Results: Cyperaceae originated in South America in the late Cretaceous and subsequently dispersed throughout the globe. Of three increases in diversification rate, two occurred in the temperate Northern Hemisphere. The variable most closely associated with clade richness is the partitioning of geographical space by species within each clade. Main conclusions: We show that species-rich clades in Cyperaceae are not only more widespread, occupy more niche space, and diversify more quickly, but also exhibit patterns that are consistent with the partitioning of geographical and ecological space as a major correlate to diversification. [ABSTRACT FROM AUTHOR]

Aim To examine the role of geological history, connectivity and distance in shaping the biogeographical structure of North American desert clades that are restricted to habitat islands (sand dunes and relictual aquatic habitats), using statistical model choice on old and new probabilistic biogeographical models. Location North America, Mojave, Sonoran and Chihuahuan Deserts. Materials and methods Dated phylogenies were estimated for three field-sampled insect clades ( Trigonoscuta, Rhaphiomidas and sand treader crickets), and five other literature-sampled clades (the snails Assiminea, Pyrgulopsis and Tryonia; the desert fringe-toed lizard Uma; and the desert pupfish Cyprinodon). BioGeo BEARS was used to statistically compare biogeographical models assuming unconstrained or connectivity-constrained dispersal, with or without founder-event speciation (jump dispersal) permitted. Finally, we introduce and test a novel distance-based dispersal model (+x) where dispersal probability is multiplied by distance to the power x. Results We observed little concordance between biogeographical patterns and timing of geological events. Model comparisons were decidedly in favour of inclusion of founder-event speciation in the models for most taxa, with only a small taxon, Uma, showing support for the model favouring vicariance. The inclusion of a constrained-dispersal matrix was favoured by three of the eight taxa examined ( Cyprinodon, sand treader crickets, and Trigonoscuta). Surprisingly, tests for distance influencing dispersal probability were mostly negative. Main conclusions Our results do not show support for any one geological event shaping the biogeographical patterns of these desert taxa. Instead, the histories of desert dune and aquatic taxa are largely products of rare jump dispersal events, and can be considered island-like systems. Although results are negative for the distance-based dispersal model, this in itself demonstrates the superiority of explicit statistical model testing over a priori assumption of fixed models in historical biogeography. [ABSTRACT FROM AUTHOR]

Brassicales is a diverse order perhaps most famous because it houses Brassicaceae and, its premier member, Arabidopsis thaliana . This widely distributed and species-rich lineage has been overlooked as a promising system to investigate patterns of disjunct distributions and diversification rates. We analyzed plastid and mitochondrial sequence data from five gene regions (>8000 bp) across 151 taxa to: (1) produce a chronogram for major lineages in Brassicales, including Brassicaceae and Arabidopsis , based on greater taxon sampling across the order and previously overlooked fossil evidence, (2) examine biogeographical ancestral range estimations and disjunct distributions in BioGeoBEARS, and (3) determine where shifts in species diversification occur using BAMM. The evolution and radiation of the Brassicales began 103 Mya and was linked to a series of inter-continental vicariant, long-distance dispersal, and land bridge migration events. North America appears to be a significant area for early stem lineages in the order. Shifts to Australia then African are evident at nodes near the core Brassicales, which diverged 68.5 Mya (HPD = 75.6–62.0). This estimated age combined with fossil evidence, indicates that some New World clades embedded amongst Old World relatives (e.g., New World capparoids) are the result of different long distance dispersal events, whereas others may be best explained by land bridge migration (e.g., Forchhammeria ). Based on these analyses, the Brassicaceae crown group diverged in Europe/Northern Africa in the Eocene, circa 43.4 Mya (HPD = 46.6–40.3) and Arabidopsis separated from close congeners circa 10.4 Mya. These ages fall between divergent dates that were previously published, suggesting we are slowly converging on a robust age estimate for the family. Three significant shifts in species diversification are observed in the order: (1) 58 Mya at the crown of Capparaceae, Cleomaceae and Brassicaceae, (2) 38 Mya at the crown of Resedaceae + Stixis clade, and (3) 21 Mya at the crown of the tribes Brassiceae and Sisymbrieae within Brassicaceae. [ABSTRACT FROM AUTHOR]

The harvestmen genus Calicina is represented by 25 short-range endemic species occurring in the western Sierra Nevada, Transverse and Coast Ranges of California. Our principal aim was to reconstruct the temporal and spatial biogeographic history of this arachnid lineage. We inferred a time-calibrated species tree for 21 of 25 described Calicina species using multiple genes and multilocus coalescent-based methods. This species tree was used as a framework for algorithmic biogeographic and divergence time analyses, and a phylogenetic canonical correlation analysis (CCA) was used to examine the relationship between morphological evolution and environmental variables. Species tree and biogeographic analyses indicate that high-elevation Sierran taxa are early-diverging in Calicina , with subsequent biogeographic “criss-crossing” of lineages from the Sierra Nevada to the Coast Ranges, back to the Sierra Nevada, then back to Coast Ranges. In both the Sierra Nevada and Coast Ranges, distantly-related parapatric lineages essentially never occur in sympatry. CCA reveals that in both the Coast Ranges and the Sierra Nevada, distant phylogenetic relatives evolve convergent morphologies. Our evidence shows that Calicina is clearly dispersal-limited, with an ancient biogeographic history that provides unique insight into the complex geologic evolution of California since the mid-Paleogene. [ABSTRACT FROM AUTHOR]

Although it is an uncommon distribution in seed plants, many bryophytes occur around the Pacific Rim of north-western North America and eastern Asia. This work focuses on a clade of peatmosses ( Sphagnum) that is distributed around the Pacific Rim region, with some individual species found across the total range. The goals were to infer divergent phylogenetic relationships among haploid species in the clade, assess parentage of allopolyploid taxa, and evaluate alternative hypotheses about inter- and intraspecific geographical range evolution. Multiple data sets and analyses resolved an 'Alaska' clade, distributed across western North America, eastern China and Japan, and an 'Asia' clade that includes western Chinese, Thai, Korean, eastern Chinese and Japanese lineages. Allopolyploids have arisen at least four times in the Pacific Rim clade of Sphagnum subgen. Subsecunda; it appears that all allopolyploid origins involved closely related haploid parental taxa. Biogeographical inferences were impacted by topological uncertainty and especially by the biogeographical model utilized to reconstruct ancestral areas. Most analyses converge on the conclusion that the ancestor to this clade of Pacific Rim Sphagnum species was widespread from Alaska south to eastern Asia, but a northern origin for the Alaska subclade was supported by one of the two biogeographical models we employed, under which it was robust to phylogenetic uncertainty. [ABSTRACT FROM AUTHOR]

In the California Floristic Province (CA-FP) and nearby deserts, 19 species of Salvia (Lamiaceae, Mentheae) form a small radiation but an important component of the chaparral and desert communities. Traditionally, two groups within these Californian Salvia have been recognized (usually treated as sections), but relationships within each, to each other, and to other Salvia are unclear. Phylogenetic relationships of all species, with multiple accessions for most, were obtained using chloroplast DNA (cpDNA) and nuclear ribosomal DNA (nrDNA) markers. Ancestral character state reconstruction of both vegetative and floral features was done on the resulting nrDNA tree. Biogeographical analysis of the groups within the CA-FP and adjacent floristic provinces was done in BioGeoBEARS and species diversification assessed with BAMM. Significant conclusions drawn from the study include: 1) California Salvia should be classified into two monophyletic sections, Audibertia (15 species) and Echinosphace, (four species) in the new subgenus Audibertia; 2) subg. Audibertia and the Neotropical subg. Calosphace are sister clades, most closely related to Asian groups, and are likely Asian in origin; 3) nrDNA provides a fairly resolved tree for subg. Audibertia with all species monophyletic; 4) cpDNA and nrDNA trees are strongly incongruent and provide evidence that hybridization and chloroplast capture have played an important role in the evolution of subg. Audibertia; 5) ancestral character reconstruction of states in habit, possession of spines, calyx lobing, and staminal features highlights a complex (sometimes convergent) evolutionary history of this iconic CA-FP lineage; 6) subg. Audibertia arose in desert areas and more recently diversified into the southwestern California region and adjacent regions with the formation of the Mediterranean-like climate; and 7) this diversification exhibits a slight decrease in speciation and an increase in extinction rates over the group's 11 million year history. [ABSTRACT FROM AUTHOR]

Founder-event speciation, where a rare jump dispersal event founds a new genetically isolated lineage, has long been considered crucial by many historical biogeographers, but its importance is disputed within the vicariance school. Probabilistic modeling of geographic range evolution creates the potential to test different biogeographical models against data using standard statistical model choice procedures, as long as multiple models are available. I re-implement the Dispersal–Extinction–Cladogenesis (DEC) model of LAGRANGE in the R package BioGeoBEARS, and modify it to create a new model, DEC + J, which adds founder-event speciation, the importance of which is governed by a new free parameter, j. The identifiability of DEC and DEC + J is tested on data sets simulated under a wide range of macroevolutionary models where geography evolves jointly with lineage birth/death events. The results confirm that DEC and DEC + J are identifiable even though these models ignore the fact that molecular phylogenies are missing many cladogenesis and extinction events. The simulations also indicate that DEC will have substantially increased errors in ancestral range estimation and parameter inference when the true model includes + J. DEC and DEC + J are compared on 13 empirical data sets drawn from studies of island clades. Likelihood-ratio tests indicate that all clades reject DEC, and AICc model weights show large to overwhelming support for DEC + J, for the first time verifying the importance of founder-event speciation in island clades via statistical model choice. Under DEC + J, ancestral nodes are usually estimated to have ranges occupying only one island, rather than the widespread ancestors often favored by DEC. These results indicate that the assumptions of historical biogeography models can have large impacts on inference and require testing and comparison with statistical methods. [ABSTRACT FROM AUTHOR]

Event-based biogeographic methods, such as dispersal-extinction-cladogenesis, have become increasingly popular for attempting to reconstruct the biogeographic history of organisms. Such methods employ distributional data of sampled species and a dated phylogenetic tree to estimate ancestral distribution ranges. Because the input tree is often a single consensus tree, uncertainty in topology and age estimates are rarely accounted for, even when they may affect the outcome of biogeographic estimates. Even when such uncertainties are taken into account for estimates of ancestral ranges, they are usually ignored when researchers compare competing biogeographic hypotheses. We explore the effect of incorporating this uncertainty in a biogeographic analysis of the 21 species of sand spiders (Sicariidae: Sicarius) from Neotropical xeric biomes, based on a total-evidence phylogeny including a complete sampling of the genus. Using a custom R script, we account for uncertainty in ages and topology by estimating ancestral ranges over a sample of trees from the posterior distribution of a Bayesian analysis, and for uncertainty in biogeographic estimates by using stochastic maps. This approach allows for counting biogeographic events such as dispersal among areas, counting lineages through time per area, and testing biogeographic hypotheses, while not overestimating the confidence in a single topology. Including uncertainty in ages indicates that Sicarius dispersed to the Galapagos Islands when the archipelago was formed by paleo-islands that are now submerged; model comparison strongly favors a scenario where dispersal took place before the current islands emerged. We also investigated past connections among currently disjunct Neotropical dry forests; failing to account for topological uncertainty underestimates possible connections among the Caatinga and Andean dry forests in favor of connections among Caatinga and Caribbean + Mesoamerican dry forests. Additionally, we find that biogeographic models including a founder-event speciation parameter ("+J") are more prone to suffer from the overconfidence effects of estimating ancestral ranges using a single topology. This effect is alleviated by incorporating topological and age uncertainty while estimating stochastic maps, increasing the similarity in the inference of biogeographic events between models with or without a founder-event speciation parameter. We argue that incorporating phylogenetic uncertainty in biogeographic hypothesis-testing is valuable and should be a commonplace approach in the presence of rogue taxa or wide confidence intervals in age estimates, and especially when using models including founder-event speciation. [ABSTRACT FROM AUTHOR]

• Detected 4 main lineages originated in the Miocene in the African continent. • Saharo-Sindian lineages evolved separately from Palaearctic and Afrotropical Region. • Oriental Region: colonized after dispersal event from the Afrotropical Region. • The genus Hycleus includes also the genera Ceroctis and Paractenodia. • No subgeneric division was found, but some phenetic groups resulted well supported. Hycleus is a hyper-diverse genus of blister beetles including ~500 species widely distributed in the Old World, currently divided into three "sections" and into 45 "phenetic" species groups according to morphological characters. Recently the monophyly of Hycleus was questioned pointing out its paraphyly with respect to the genera Ceroctis and Paractenodia. In this study, we built a time-calibrated phylogenetic tree based on DNA sequence data from mitochondrial and nuclear genes obtained from 125 species, to understand the phylogenetic relationships among the species of this genus, to infer the biogeographic processes behind their diversification, and to assess their taxonomy and classification. Our results identified four main lineages one of which included the species belonging to Ceroctis and Paractenodia ; therefore, both taxa are now referred to Hycleus as new synonyms. The three described sections of Hycleus resulted polyphyletic and are rejected, whereas several species groups represented well supported clades. Hycleus likely originated in Africa during the Early Miocene (~20 Mya), and subsequently spread in Europe and western Asia. Later, in the Late Miocene (~6 Mya) a Saharo-Sindian group branched off from the Palaearctic lineage, whereas the Oriental Region was colonized following a dispersal event through the Arabian Peninsula from the Afrotropical Region (~5 Mya). [ABSTRACT FROM AUTHOR]