No full-text available
To read the full-text of this research,
you can request a copy directly from the authors.
Fossils constrain biogeographical history in a clade of flattened spiders with transcontinental distribution
Journal of Biogeography
Abstract
Aim
Fossil data may be crucial to infer biogeographical history, especially in taxa with tropical trans-Pacific distributions. Here, we use extinct and extant trochanteriid flattened spiders to test hypotheses that could explain its trans-Pacific disjunct distribution, including a Boreotropical origin with a North Atlantic dispersal, an African origin with South Atlantic dispersal and an Eurasian origin with Bering Bridge route.
Location
World-wide.
Taxon
Trochanteriidae, Plator-Doliomalus-Vectius (PDV) clade.
Methods
MicroCT was used to collect morphological data from an undescribed Baltic amber fossil. These data were used with additional fossils and extant species in a total-evidence, tip-dated phylogenetic analysis. We tested different scenarios using constrained dispersal matrices in a Bayesian approach. An analysis with fossils pruned was also performed to explore how lack of fossil data might impact inferences of biogeographical process.
Results
The phylogenetic analyses allowed us to place the new fossil in the genus Plator. Analyses without fossils suggest an African origin with a dispersal to Asia from India and a South Atlantic dispersal to South America. When fossils are included, hypothesis-testing rejects this scenario and equally supports a Boreotropical and an Afro-European origin with a South Atlantic route and a dispersal to Asia from Europe.
Main conclusions
Biogeographical inferences of disjunctly distributed taxa should be interpreted with caution when fossils are not included. Although one alternative hypothesis was not completely rejected, results show that the Boreotropical hypothesis for the PDV clade could be a robust explanation for its actual distribution. This hypothesis is mostly overlooked in animal taxa and rigorous tests with other taxa with similar distributions may reveal that a Boreotropical origin is common. We discuss methodological approaches that could improve biogeographical tests using fossils as terminals.
... Because of such patterns, the importance of fossils for biogeographical studies has been appreciated for more than a century [2]. Nevertheless, inclusion of fossil data in model-based biogeographical analyses of extant taxa remains limited to just a few remarkable examples in the literature [12][13][14][15][16][17][18][19][20][21]. ...
The separation of closely related terrestrial or freshwater species by vast marine barriers represents a biogeographical riddle. Such cases can provide evidence for vicariance, a process whereby ancient geological events like continental rifting divided ancestral geographical ranges. With an evolutionary history extending tens of millions of years, freshwater ecology, and distribution encompassing widely separated southern landmasses, osteoglossid bonytongue fishes are a textbook case of vicariance attributed to Mesozoic fragmentation of the Gondwanan supercontinent. Largely overlooked fossils complicate the clean narrative invoked for extant species by recording occurrences on additional continents and in marine settings. Here, we present a new total-evidence phylogenetic hypothesis for bonytongue fishes combined with quantitative models of range evolution and show that the last common ancestor of extant osteoglossids was likely marine, and that the group colonized freshwater settings at least four times when both extant and extinct lineages are considered. The correspondence between extant osteoglossid relationships and patterns of continental fragmentation therefore represents a striking example of biogeographical pseudocongruence. Contrary to arguments against vicariance hypotheses that rely only on temporal or phylogenetic evidence, these results provide direct palaeontological support for enhanced dispersal ability early in the history of a group with widely separated distributions in the modern day.
... Similar to the molecular model in the dating analyses (above), we did not test other biogeographical models (such as DIVA-like and BayArea-like), because DEC includes all other models (Ree and Smith, 2008;Matzke, 2013) and, in a Bayesian analysis, can account for parameter uncertainty when testing each biogeographic hypothesis. The J parameter (jump dispersal; Matzke, 2013) was not included for reasons discussed in Ree and Sanmartín (2018) and commented on in Azevedo et al. (2021) (but see Matzke, 2022). Models with the jump dispersal parameter may underestimate anagenetic range dispersal (which is important to test our hypothesis here) and be statistically degenerate, and the probability of a jump dispersal (i.e., a dispersal quickly followed by a vicariance) is already modeled in the regular DEC model. ...
... The Trochanteriidae Karsch, 1879 is a relatively small spider family with six genera and 50 species currently known worldwide (World Spider Catalog 2022). Members of this group are commonly known as flattened spiders due to their dorsoventrally flattened bodies which may be an adaptation to life in cracks and under tree barks (Zhu and Zhang 2011;Azevedo et al. 2021). The mitochondrial genomes have provided valuable insights on the evolution of various animal groups (e.g. ...
Plator insolens Simon, 1880 belongs to the family Trochanteriidae and is distributed in China. Herein, we report the complete mitochondrial genome of P. insolens reconstructed from Illumina sequencing data, which is the first published mitochondrial genome for the family. The mitogenome is 14,519 bp in length and contains 13 protein-coding genes, 22 transfer RNA genes and two ribosomal RNA genes. The phylogenetic analysis indicates that P. insolens is clustered within the RTA clade of the infraorder Araneomorphae. This study provides useful genetic information for future studies on the taxonomy, phylogeny and evolution of trochanteriid species.
... Plator, Platyoides, Trochanteria, Vectius, and, provisionally, Hemicloea. The Australian Hemicloea could be closely related to members of Lamponidae, Gnaphosidae or Trochanteriidae, as found here and in previous studies (Azevedo et al., 2021;Azevedo et al., 2018;Platnick, 2002;Wheeler et al., 2017). It is unlikely that Hemicloea is closely related to the Australian flattened dionychans now placed in the Trachycosmidae n. rank, since no phylogenetic analyses so far suggested this relationship. ...
The importance of morphology in the phylogenomic era has recently gained attention, but relatively few studies have combined both types of information when inferring phylogenetic relationships. Sanger sequencing legacy data can also be important for understanding evolutionary relationships. The possibility of combining genomic, morphological and Sanger data in one analysis seems compelling, permitting a more complete sampling and yielding a comprehensive view of the evolution of a group. Here we used these three data types to elucidate the systematics and evolution of the Dionycha, a highly diverse group of spiders relatively underrepresented in phylogenetic studies. The datasets were analyzed separately and combined under different inference methods, including a novel approach for analyzing morphological matrices with commonly used evolutionary models. We tested alternative hypotheses of relationships and performed simulations to investigate the accuracy of our findings. We provide a comprehensive and thorough phylogenetic hypothesis for Dionycha that can serve as a robust framework to test hypotheses about the evolution of key characters. We also show that morphological data might have a phylogenetic impact, even when massively outweighed by molecular data. Our approach to analyze morphological data may serve as an alternative to the proposed practice of arbitrarily partitioning, weighting, and choosing between parsimony and stochastic models. As a result of our findings, we propose Trachycosmidae new rank for a group of Australian genera formerly included in Trochanteriidae and Gallieniellidae, and consider Ammoxenidae as a junior synonym of Gnaphosidae. We restore the family rank for Prodidomidae, but transfer the subfamily Molycriinae to Gnaphosidae. Drassinella is transferred to Liocranidae, Donuea to Corinnidae, and Mahafalytenus to Viridasiidae.
Recluse or violin spiders in the genus Loxosceles (Scytodoidea: Sicariidae) are a diverse group (~140 extant species) including medically important species and distributed mainly in the Americas, Africa, and the Mediterranean region. In addition, this genus includes three fossil species from Miocene Dominican amber. Here we revise the taxonomy of these fossil species by examining, imaging and re-describing their type specimens. We find that L. defecta Wunderlich, 1988 and L. deformis Wunderlich, 1988 are bona fide members of the genus and report additional characters overlooked in their original descriptions. We further study the ho-lotype of L. aculicaput Wunderlich, 2004 using synchrotron radiation micro-computed tomography to reveal previously unknown morphological details hidden by fissures in the amber. We found several characters inconsistent with Loxosceles but consistent with Drymusa (false violin spiders; Scytodoidea: Drymusidae), such as three claws, well-developed podotarsite, and a broad colulus. This suggests the species is misplaced in Loxosceles. To test this hypothesis, we estimated a total-evidence phylogeny of the superfamily Scytodoidea including extant and fossil taxa, morphological data, traditional molecular markers, and sequences of ultra-conserved elements. The results show unambiguously that L. aculicaput belongs to Drymusa and is a close relative of extant species of the genus inhabiting the Greater Antilles. Therefore, we here transfer this species to Drymusa, establishing a new combination and new family assignment. Drymusa aculicaput comb. nov. represents the first known fossil Drymusidae and shows that crown members of this genus already existed in the Miocene.
Over the past decade, a new set of methods for estimating dated trees has emerged. Originally referred to as the fossilized birth–death (FBD) process, this single model has expanded to a family of models that allows researchers to coestimate evolutionary parameters (e.g., diversification, sampling) and patterns alongside divergence times for a variety of applications from paleobiology to real-time epidemiology. We provide an overview of this family of models. We explore the ways in which these models correspond to methods in quantitative paleobiology, as the FBD process provides a framework through which neontological and paleontological approaches to phylogenetics and macroevolution can be unified. We also provide an overview of challenges associated with applying FBD models, particularly with an eye toward the fossil record. We conclude this piece by discussing several exciting avenues for the inclusion of fossil data in phylogenetic analyses.
Expected final online publication date for the Annual Review of Ecology, Evolution, and Systematics, Volume 53 is November 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
Phylogenomic and paleontological data constitute complementary resources for unravelling the phylogenetic relationships and divergence times of lineages, yet few studies have attempted to fully integrate them. Several unique properties of echinoids (sea urchins) make them especially useful for such synthetizing approaches, including a remarkable fossil record that can be incorporated into explicit phylogenetic hypotheses. We revisit the phylogeny of crown group Echinoidea using a total-evidence dating approach that combines the largest phylogenomic dataset for the clade, a large-scale morphological matrix with a dense fossil sampling, and a novel compendium of tip and node age constraints. To this end, we develop a novel method for subsampling phylogenomic datasets that selects loci with high phylogenetic signal, low systematic biases and enhanced clock-like behavior. Our results demonstrate that combining different data sources increases topological accuracy and helps resolve conflicts between molecular and morphological data. Notably, we present a new hypothesis for the origin of sand dollars, and restructure the relationships between stem and crown echinoids in a way that implies a long stretch of undiscovered evolutionary history of the crown group in the late Paleozoic. Our efforts help bridge the gap between phylogenomics and phylogenetic paleontology, providing a model example of the benefits of combining the two.
Time calibrated trees are challenging to estimate for many extinct groups of species due to the incompleteness of the rock and fossil records. Additionally, the precise age of a sample is typically not known as it may have occurred at any time during the time interval spanned by the rock layer. Bayesian phylogenetic approaches provide a coherent framework for incorporating multiple sources of evidence and uncertainty. In this study, we simulate datasets with characteristics typical of Palaeozoic marine invertebrates, in terms of character and taxon sampling. We use these datasets to examine the impact of different age handling methods on estimated topologies and divergence times obtained using the fossilized birth-death process. Our results reiterate the importance of modeling fossil age uncertainty, although we find that the relative impact of fossil age uncertainty depends on both fossil taxon sampling and character sampling. Sampling the fossil ages as part of the inference gives topology and divergence time estimates that are as good as those obtained by fixing ages to the truth, whereas fixing fossil ages to incorrect values results in higher error and lower coverage. The relative effect increases with increased fossil and character sampling. Modeling fossil age uncertainty is thus critical, as fixing incorrect fossil ages will negate the benefits of improved fossil and character sampling.
Studies in evolutionary biology and biogeography increasingly rely on the estimation of dated phylogenetic trees using molecular clocks. In turn, the calibration of such clocks is critically dependent on external evidence (i.e. fossils) anchoring the ages of particular nodes to known absolute ages. In recent years, a plethora of new fossil spiders, especially from the Mesozoic, have been described, while the number of studies presenting dated spider phylogenies based on fossil calibrations increased sharply. We critically evaluate 44 of these studies, which collectively employed 67 unique fossils in 180 calibrations. Approximately 54% of these calibrations are problematic, particularly regarding unsupported assignment of fossils to extant clades (44%) and crown (rather than stem) dating (9%). Most of these cases result from an assumed equivalence between taxonomic placement of fossils and their phylogenetic position. To overcome this limitation, we extensively review the literature on fossil spiders, with a special focus on putative synapomorphies and the phylogenetic placement of fossil species with regard to their importance for calibrating higher taxa (families and above) in the spider tree of life. We provide a curated list including 41 key fossils intended to be a basis for future estimations of dated spider phylogenies. In a second step, we use a revised set of 23 calibrations to estimate a new dated spider tree of life based on transcriptomic data. The revised placement of key fossils and the new calibrated tree are used to resolve a long‐standing debate in spider evolution – we tested whether there has been a major turnover in the spider fauna between the Mesozoic and Cenozoic. At least 17 (out of 117) extant families have been recorded from the Cretaceous, implying that at least 41 spider lineages in the family level or above crossed the Cretaeous–Paleogene (K–Pg) boundary. The putative phylogenetic affinities of families known only from the Mesozoic suggest that at least seven Cretaceous families appear to have no close living relatives and might represent extinct lineages. There is no unambiguous fossil evidence of the retrolateral tibial apophysis clade (RTA‐clade) in the Mesozoic, although molecular clock analyses estimated the major lineages within this clade to be at least ∼100 million years old. Our review of the fossil record supports a major turnover showing that the spider faunas in the Mesozoic and the Cenozoic are very distinct at high taxonomic levels, with the Mesozoic dominated by Palpimanoidea and Synspermiata, while the Cenozoic is dominated by Araneoidea and RTA‐clade spiders.
Elaboration of Bayesian phylogenetic inference methods has continued at pace in recent years with major new advances in nearly all aspects of the joint modelling of evolutionary data. It is increasingly appreciated that some evolutionary questions can only be adequately answered by combining evidence from multiple independent sources of data, including genome sequences, sampling dates, phenotypic data, radiocarbon dates, fossil occurrences, and biogeographic range information among others. Including all relevant data into a single joint model is very challenging both conceptually and computationally. Advanced computational software packages that allow robust development of compatible (sub-)models which can be composed into a full model hierarchy have played a key role in these developments. Developing such software frameworks is increasingly a major scientific activity in its own right, and comes with specific challenges, from practical software design, development and engineering challenges to statistical and conceptual modelling challenges. BEAST 2 is one such computational software platform, and was first announced over 4 years ago. Here we describe a series of major new developments in the BEAST 2 core platform and model hierarchy that have occurred since the first release of the software, culminating in the recent 2.5 release.
The exchange of biotas between Eurasia and North America across the Bering Land Bridge had a major impact on ecosystems of both continents throughout the Cenozoic. This exchange has received particular attention regarding placental mammals dispersing into the Americas, including humans after the last glacial period, and also as an explanation for the disjunct distribution of related seed plants in eastern Asia and eastern North America. Here we investigated the bi-directional dispersal across the Bering Land Bridge from estimates of dispersal events based on time-calibrated phylogenies of a broad range of plant, fungus, and animal taxa. We revealed a long-lasting phase of asymmetrical biotic interchange, with a peak of dispersal from Asia into North America during the Late Oligocene warming (26–24 Ma), when dispersal in the opposite direction was greatly decreased. Influx from North America into Asia was lower than in the opposite direction throughout the Cenozoic, but with peak rates of dispersal at the end of the Eocene (40–34 Ma) and again in the Early to Middle Miocene (16–14 Ma). The strong association between dispersal patterns and environmental changes suggests that plants, fungi, and animals have likely dispersed from stable to perturbed environments of North America and Eurasia throughout the Cenozoic.
The bony-tongue fishes, Osteoglossomorpha, have been the focus of a great deal of morphological, systematic, and evolutionary study, due in part to their basal position among extant teleostean fishes. This group includes the mooneyes (Hiodontidae), knifefishes (Notopteridae), the abu (Gymnarchidae), elephantfishes (Mormyridae), arawanas and pirarucu (Osteoglossidae), and the African butterfly fish (Pantodontidae). This morphologically heterogeneous group also has a long and diverse fossil record, including taxa from all continents and both freshwater and marine deposits. The phylogenetic relationships among most extant osteoglossomorph families are widely agreed upon. However, there is still much to discover about the systematic biology of these fishes, particularly with regard to the phylogenetic affinities of several fossil taxa, within Mormyridae, and the position of Pantodon. In this paper we review the state of knowledge for osteoglossomorph fishes. We first provide an overview of the diversity of Osteoglossomorpha, and then discuss studies of the phylogeny of Osteoglossomorpha from both morphological and molecular perspectives, as well as biogeographic analyses of the group. Finally, we offer our perspectives on future needs for research on the systematic biology of Osteoglossomorpha.
Keywords:
Biogeography; Osteoglossidae; Paleontology; Phylogeny; Taxonomy
Sloths, like other xenarthrans, are an extremely interesting group of mammals that, after a long history of evolution and diversification in South America, became established on islands in the Caribbean and later reached North America during the Great American Biotic Interchange. In all three regions, they were part of the impressive Pleistocene megafauna. Most taxa became extinct and only two small, distantly related tree-dwelling genera survived. Here we incorporate several recently described genera of sloths into an assembled morphological data supermatrix and apply Bayesian inference, using phylogenetic and morphological clock methods, to 64 sloth genera. Thus, we investigate the evolution of the group in terms of the timing of divergence of different lineages and their diversity, morphological disparity and biogeographical history. The phylogeny obtained supports the existence of the commonly recognized clades for the group. Our results provide divergence time estimates for the major clades within Folivora that could not be dated with molecular methods. Lineage diversity shows an early increase, reaching a peak in the Early Miocene followed by a major drop at the end of the Santacrucian (Early Miocene). A second peak in the Late Miocene was also followed by a major drop at the end of the Huayquerian (Late Miocene). Both events show differential impact at the family level. After that, a slight Plio-Pleistocene decline was observed before the marked drop with the extinction at the end of the Pleistocene. Phenotypic evolutionary rates were high during the early history of the clade, mainly associated with Mylodontidae, but rapidly decreased to lower values around 25 Ma, whereas Megalonychidae had lower rates at the beginning followed by a steady increase, peaking during the Late Miocene and the Pliocene. Morphological disparity showed a similar trend, with an early increase, followed by a slowly increasing phase through the Late Oligocene and Early Miocene, and ending with another increase beginning at the middle of the Miocene. Biogeographic analysis showed southern South America as the most probable area of origin of the clade and the main region in which the early diversification events took place. Both Megatheriinae and Nothrotheriinae basal nodes were strongly correlated with Andean uplift events, whereas the early history of Mylodontidae is closely associated with southern South America and also shows an early occupation of the northern regions. Within Megalonychidae, our results show Choloepus as a descendant of an island dispersing ancestor and a probable re-ingression to South America by a clade that originated in Central or North America.
The Hawaiian silversword alliance (Asteraceae) is an iconic adaptive radiation. However, like many island plant lineages, no fossils have been assigned to the clade. As a result, the clade's age and diversification rate are not known precisely, making it difficult to test biogeographic hypotheses about the radiation. In lieu of fossils, paleogeographically structured biogeographic processes may inform species divergence times; for example, an island must first exist for a clade to radiate upon it. We date the silversword clade and test biogeographic hypotheses about its radiation across the Hawaiian Archipelago by modeling interactions between species relationships, molecular evolution, biogeographic scenarios, divergence times, and island origination times using the Bayesian phylogenetic framework, RevBayes. The ancestor of living silverswords most likely colonized the modern Hawaiian Islands once from the mainland approximately 5.1 Ma, with the most recent common ancestor of extant silversword lineages first appearing approximately 3.5 Ma. Applying an event‐based test of the progression rule of island biogeography, we found strong evidence that the dispersal process prefers old‐to‐young directionality, but strong evidence for diversification continuing unabated into later phases of island ontogeny, particularly for Kaua‘i. This work serves as a general example for how diversification studies benefit from incorporating biogeographic and paleogeographic components.
This article is protected by copyright. All rights reserved
Morphological, mitochondrial, and nuclear phylogenomic data were combined to address phylogenetic and species delimitation questions in cave-limited Cicurina spiders from central Texas. Special effort was focused on specimens and cave locations in the San Antonio region (Bexar County), home to four eyeless species listed as US Federally Endangered. Sequence capture experiments resulted in the recovery of ~200–400 homologous ultra-conserved element (UCE) nuclear loci across taxa, and nearly complete COI mitochondrial DNA sequences from the same set of individuals. Some of these nuclear and mitochondrial sequences were recovered from “standard” museum specimens without special preservation of DNA material, including museum specimens preserved in the 1990s. Multiple phylogenetic analyses of the UCE data agree in the recovery of two major lineages of eyeless Cicurina in Texas. These lineages also differ in mitochondrial clade membership, female genitalic morphology, degree of troglomorphy (as measured by relative leg length), and are mostly allopatric across much of Texas. Rare sympatry was confirmed in Bexar County, where members of the two major clades sometimes co-exist in the same karst feature. Both nuclear phylogenomic and mitochondrial data indicate the existence of undescribed species from the San Antonio region, although further sampling and collection of adult specimens is needed to explicitly test these hypotheses. Our data support the two following species synonymies ( Cicurinavenii Gertsch, 1992 = Cicurinamadla Gertsch, 1992; Cicurinaloftini Cokendolpher, 2004 = Cicurinavespera Gertsch, 1992), formally proposed here. Overall, our taxonomy-focused research has many important conservation implications, and again highlights the fundamental importance of robust taxonomy in conservation research.
Bayesian inference of phylogeny using Markov chain Monte Carlo (MCMC) (Drummond et al., 2002; Mau et al., 1999; Rannala and Yang, 1996) flourishes as a popular approach to uncover the evolutionary relationships among taxa, such as genes, genomes, individuals or species. MCMC approaches generate samples of model parameter values - including the phylogenetic tree -drawn from their posterior distribution given molecular sequence data and a selection of evolutionary models. Visualising, tabulating and marginalising these samples is critical for approximating the posterior quantities of interest that one reports as the outcome of a Bayesian phylogenetic analysis. To facilitate this task, we have developed the Tracer (version 1.7) software package to process MCMC trace files containing parameter samples and to interactively explore the high-dimensional posterior distribution. Tracer works automatically with sample output from BEAST (Drummond et al., 2012), BEAST2 (Bouckaert et al., 2014), LAMARC (Kuhner, 2006), Migrate (Beerli, 2006), MrBayes (Ronquist et al., 2012), RevBayes (Höhna et al., 2016) and possibly other MCMC programs from other domains.
Phylogenetic studies of geographic range evolution are increasingly using statistical model selection methods to choose among variants of the dispersal-extinction-cladogenesis (DEC) model, especially between DEC and DEC+J, a variant that emphasizes “jump dispersal,” or founder-event speciation, as a type of cladogenetic range inheritance scenario. Unfortunately, DEC+J is a poor model of founder-event speciation, and statistical comparisons of its likelihood with DEC are inappropriate. DEC and DEC+J share a conceptual flaw: cladogenetic events of range inheritance at ancestral nodes, unlike anagenetic events of dispersal and local extinction along branches, are not modelled as being probabilistic with respect to time. Ignoring this probability factor artificially inflates the contribution of cladogenetic events to the likelihood, and leads to underestimates of anagenetic, time-dependent range evolution. The flaw is exacerbated in DEC+J because not only is jump dispersal allowed, expanding the set of cladogenetic events, its probability relative to non-jump events is assigned a free parameter, j, that when maximized precludes the possibility of non-jump events at ancestral nodes. DEC+J thus parameterizes the mode of speciation, but like DEC, it does not parameterize the rate of speciation. This inconsistency has undesirable consequences, such as a greater tendency towards degenerate inferences in which the data are explained entirely by cladogenetic events (at which point branch lengths become irrelevant, with estimated anagenetic rates of 0). Inferences with DEC+J can in some cases depart dramatically from intuition, e.g. when highly unparsimonious numbers of jump dispersal events are required solely because j is maximized. Statistical comparison with DEC is inappropriate because a higher DEC+J likelihood does not reflect a more close approximation of the “true” model of range evolution, which surely must include time-dependent processes; instead, it is simply due to more weight being allocated (via j) to jump dispersal events whose time-dependent probabilities are ignored. In testing hypotheses about the geographic mode of speciation, jump dispersal can and should instead be modelled using existing frameworks for state-dependent lineage diversification in continuous time, taking appropriate cautions against Type I errors associated with such methods. For simple inference of ancestral ranges on a fixed phylogeny, a DEC-based model may be defensible if statistical model selection is not used to justify the choice, and it is understood that inferences about cladogenetic range inheritance lack any relation to time, normally a fundamental axis of evolutionary models.
We present a phylogenetic analysis of spiders using a dataset of 932 spider species, representing 115 families (only the family Synaphridae is unrepresented), 700 known genera, and additional representatives of 26 unidentified or undescribed genera. Eleven genera of the orders Amblypygi, Palpigradi, Schizomida and Uropygi are included as outgroups. The dataset includes six markers from the mitochondrial (12S, 16S, COI) and nuclear (histone H3, 18S, 28S) genomes, and was analysed by multiple methods, including constrained analyses using a highly supported backbone tree from transcriptomic data. We recover most of the higher-level structure of the spider tree with good support, including Mesothelae, Opisthothelae, Mygalomorphae and Araneomorphae. Several of our analyses recover Hypochilidae and Filistatidae as sister groups, as suggested by previous transcriptomic analyses. The Synspermiata are robustly supported, and the families Trogloraptoridae and Caponiidae are found as sister to the Dysderoidea. Our results support the Lost Tracheae clade, including Pholcidae, Tetrablemmidae, Diguetidae, Plectreuridae and the family Pacullidae (restored status) separate from Tetrablemmidae. The Scytodoidea include Ochyroceratidae along with Sicariidae, Scytodidae, Drymusidae and Periegopidae; our results are inconclusive about the separation of these last two families. We did not recover monophyletic Austrochiloidea and Leptonetidae, but our data suggest that both groups are more closely related to the Cylindrical Gland Spigot clade rather than to Synspermiata. Palpimanoidea is not recovered by our analyses, but also not strongly contradicted. We find support for Entelegynae and Oecobioidea (Oecobiidae plus Hersiliidae), and ambiguous placement of cribellate orb-weavers, compatible with their non-monophyly. Nicodamoidea (Nicodamidae plus Megadictynidae) and Araneoidea composition and relationships are consistent with recent analyses. We did not obtain resolution for the titanoecoids (Titanoecidae and Phyxelididae), but the Retrolateral Tibial Apophysis clade is well supported. Penestomidae, and probably Homalonychidae, are part of Zodarioidea, although the latter family was set apart by recent transcriptomic analyses. Our data support a large group that we call the marronoid clade (including the families Amaurobiidae, Desidae, Dictynidae, Hahniidae, Stiphidiidae, Agelenidae and Toxopidae). The circumscription of most marronoid families is redefined here. Amaurobiidae include the Amaurobiinae and provisionally Macrobuninae. We transfer Malenellinae (Malenella, from Anyphaenidae), Chummidae (Chumma) (new syn.) and Tasmarubriinae (Tasmarubrius, Tasmabrochus and Teeatta, from Amphinectidae) to Macrobuninae. Cybaeidae are redefined to include Calymmaria, Cryphoeca, Ethobuella and Willisius (transferred from Hahniidae), and Blabomma and Yorima (transferred from Dictynidae). Cycloctenidae are redefined to include Orepukia (transferred from Agelenidae) and Pakeha and Paravoca (transferred from Amaurobiidae). Desidae are redefined to include five subfamilies: Amphinectinae, with Amphinecta, Mamoea, Maniho, Paramamoea and Rangitata (transferred from Amphinectidae); Ischaleinae, with Bakala and Manjala (transferred from Amaurobiidae) and Ischalea (transferred from Stiphidiidae); Metaltellinae, with Austmusia, Buyina, Calacadia, Cunnawarra, Jalkaraburra, Keera, Magua, Metaltella, Penaoola and Quemusia; Porteriinae (new rank), with Baiami, Cambridgea, Corasoides and Nanocambridgea (transferred from Stiphidiidae); and Desinae, with Desis, and provisionally Poaka (transferred from Amaurobiidae) and Barahna (transferred from Stiphidiidae). Argyroneta is transferred from Cybaeidae to Dictynidae. Cicurina is transferred from Dictynidae to Hahniidae. The genera Neoramia (from Agelenidae) and Aorangia, Marplesia and Neolana (from Amphinectidae) are transferred to Stiphidiidae. The family Toxopidae (restored status) includes two subfamilies: Myroinae, with Gasparia, Gohia, Hulua, Neomyro, Myro, Ommatauxesis and Otagoa (transferred from Desidae); and Toxopinae, with Midgee and Jamara, formerly Midgeeinae, new syn. (transferred from Amaurobiidae) and Hapona, Laestrygones, Lamina, Toxops and Toxopsoides (transferred from Desidae). We obtain a monophyletic Oval Calamistrum clade and Dionycha; Sparassidae, however, are not dionychans, but probably the sister group of those two clades. The composition of the Oval Calamistrum clade is confirmed (including Zoropsidae, Udubidae, Ctenidae, Oxyopidae, Senoculidae, Pisauridae, Trechaleidae, Lycosidae, Psechridae and Thomisidae), affirming previous findings on the uncertain relationships of the “ctenids” Ancylometes and Cupiennius, although a core group of Ctenidae are well supported. Our data were ambiguous as to the monophyly of Oxyopidae. In Dionycha, we found a first split of core Prodidomidae, excluding the Australian Molycriinae, which fall distantly from core prodidomids, among gnaphosoids. The rest of the dionychans form two main groups, Dionycha part A and part B. The former includes much of the Oblique Median Tapetum clade (Trochanteriidae, Gnaphosidae, Gallieniellidae, Phrurolithidae, Trachelidae, Gnaphosidae, Ammoxenidae, Lamponidae and the Molycriinae), and also Anyphaenidae and Clubionidae. Orthobula is transferred from Phrurolithidae to Trachelidae. Our data did not allow for complete resolution for the gnaphosoid families. Dionycha part B includes the families Salticidae, Eutichuridae, Miturgidae, Philodromidae, Viridasiidae, Selenopidae, Corinnidae and Xenoctenidae (new fam., including Xenoctenus, Paravulsor and Odo, transferred from Miturgidae, as well as Incasoctenus from Ctenidae). We confirm the inclusion of Zora (formerly Zoridae) within Miturgidae.
Closely related organisms with transoceanic distributions have long been the focus of historical biogeography, prompting the question of whether long-distance dispersal, or tec-tonic-driven vicariance shaped their current distribution. Regarding the Southern Hemisphere continents, this question deals with the break-up of the Gondwanan landmass, which has also affected global wind and oceanic current patterns since the Miocene. With the advent of phylogenetic node age estimation and parametric bioinformatic advances, researchers have been able to disentangle historical evolutionary processes of taxa with greater accuracy. In this study, we used the coastal spider genus Amaurobioides to investigate the historical biogeographical and evolutionary processes that shaped the modern-day distribution of species of this exceptional genus of spiders. As the only genus of the subfamily Amaurobioidinae found on three Southern Hemisphere continents, its distribution is well-suited to study in the context of Gondwanic vicariance versus long-distance, trans-oceanic dispersal. Ancestral species of the genus Amaurobioides appear to have undergone several long-distance dispersal events followed by successful establishments and speciation, starting from the mid-Miocene through to the Pleistocene. The most recent common ancestor of all present-day Amaurobioides species is estimated to have originated in Africa after arriving from South America during the Miocene. From Africa the subsequent dispersals are likely to have taken place predominantly in an eastward direction. The long-distance dispersal events by Amaurobioides mostly involved transoceanic crossings, which we propose occurred by rafting, aided by the Antarctic Circumpolar Current and the West Wind Drift.
Programs for Bayesian inference of phylogeny currently implement a unique and fixed suite of models. Consequently, users of these software packages are simultaneously forced to use a number of programs for a given study, while also lacking the freedom to explore models that have not been implemented by the developers of those programs. We developed a new open-source software package, RevBayes, to address these problems. RevBayes is entirely based on probabilistic graphical models, a powerful generic framework for specifying and analyzing statistical models. Phylogenetic-graphical models can be specified interactively in RevBayes, piece by piece, using a new succinct and intuitive language called Rev. Rev is similar to the R language and the BUGS model-specification language, and should be easy to learn for most users. The strength of RevBayes is the simplicity with which one can design, specify, and implement new and complex models. Fortunately, this tremendous flexibility does not come at the cost of slower computation; as we demonstrate, RevBayes outperforms competing software for several standard analyses. Compared with other programs, RevBayes has fewer black-box elements. Users need to explicitly specify each part of the model and analysis. Although this explicitness may initially be unfamiliar, we are convinced that this transparency will improve understanding of phylogenetic models in our field. Moreover, it will motivate the search for improvements to existing methods by brazenly exposing the model choices that we make to critical scrutiny. RevBayes is freely available at http://www.RevBayes.com. [Bayesian inference; Graphical models; MCMC; statistical phylogenetics.]
Standard models of molecular evolution cannot estimate absolute speciation times alone, and require external calibrations to do so, such as fossils. Because fossil calibration methods rely on the incomplete fossil record, a great number of nodes in the tree of life cannot be dated precisely. However, many major paleogeographical events are dated, and since biogeographic processes depend on paleogeographical conditions, biogeographic dating may be used as an alternative or complementary method to fossil dating. I demonstrate how a time-stratified biogeographic stochastic process may be used to estimate absolute divergence times by conditioning on dated paleogeographical events. Informed by the current paleogeographical literature, I construct an empirical dispersal graph using 25 areas and 26 epochs for the past 540 Ma of Earth's history. Simulations indicate biogeographic dating performs well so long as paleogeography imposes constraint on biogeographic character evolution. To gauge whether biogeographic dating may be of practical use, I analyzed the well-studied turtle clade (Testudines) to assess how well biogeographic dating fares when compared to fossil-calibrated dating estimates reported in the literature. Fossil-free biogeographic dating estimated the age of the most recent common ancestor of extant turtles to be from the Late Triassic, which is consistent with fossil-based estimates. Dating precision improves further when including a root node fossil calibration. The described model, paleogeographical dispersal graph, and analysis scripts are available for use with RevBayes.
Abstract
This report describes the contents of the PALEOMAP PaleoAtlas for GPlates, describes how the maps in the PaleoAtlas were made, documents the sources of information used to make the paleogeographic maps, and provides instructions how to plot user-defined paleodata on the paleogeographic maps using the program “PaleoDataPlotter”. The PALEOMAP PaleloAtlas and the program (Mac OSX) can be downloaded at http://www.earthbyte.org/paleomap-paleoatlas-for-gplates/ .
Please cite this work as: Scotese, C.R., 2016. PALEOMAP PaleoAtlas for GPlates and the PaleoData Plotter Program, PALEOMAP Project, http://www.earthbyte.org/paleomap-paleoatlas-for-gplates/
Part I. Introduction
The PALEOMAP PaleoAtlas for GPlates consists of 91 paleogeographic maps spanning the Phanerozoic and late Neoproterozoic. Table 1 lists all the time intervals that comprise the six volumes of the PALEOMAP PaleoAtlas for GPlates. The PaleoAtlas contains one map for nearly every stage in the Phanerozoic, as well as 3 maps for the late Precambrian. The PaleoAtlas can be directly loaded into GPLates as a “Time Dependant Raster” file (see Part III, “Loading the PALEOMAP PaleoAtlas into GPlates”). A paleogeographic map is defined as a map that shows the ancient configuration of the ocean basins and continents, as well as important topographic and bathymetric features such as mountains, lowlands, shallow sea, continental shelves, and deep oceans (Figure 1, Early Cretaceous, 121.8 Ma). Ideally, a paleogeographic map would be the kind of reference map that any time traveler would like to have before embarking on a journey back through time.
Colorful paleogeographic maps may be nice to look at, but the maps become much more useful for research and teaching purposes if users can plot their own data on the maps. In this regard, user-defined paleodata can be plotted on the paleogeographic maps in two ways: 1) using GPLates tools and procedures to import symbols and labels in a GIS-format (see GPlates Tutorial 1.1: Loading and Saving Data), and 2) by loading user-defined, latitude/longitude point data “text files” using the program “PaleoDataPlotter”. The latter method is described in the Section IV, “Plotting User-Defined Data on the Paleogeographic Reconstructions”.
PaleoDataPlotter, which is provided with this report, creates a variety of geometric symbols (circles, squares, triangles, stars, plus signs, crosses, small dots, and arrows) as well as short numeric labels (up to 5 digits), that can be plotted on the paleogeographic map at user-defined latitude/longitude coordinates (Figure 2). The PaleoDataPlotter program is ideal for plotting fossil localities, geological outcrops, as well as the locations of drill sites, wells, stratigraphic sections, or any point data set whose geographic location can be specified by modern, latitude and longitude coordinates. The arrow symbol, which can be oriented according to a user-supplied azimuth, is particularly useful for plotting “vector” information such as: ocean current directions, river flow, wind directions, paleomagnetic declinations, stress fields, and instantaneous plate motions. In a future version, the PaleoDataPlotter will also be able to plot text-labels at specific latitude/longitude coordinates.
When viruses spread, outbreaks can be spawned in previously unaffected regions. Depending on the time and mode of introduction, each regional outbreak can have its own epidemic dynamics. The migration and phylodynamic processes are often intertwined and need to be taken into account when analyzing temporally and spatially structured virus data. In this article, we present a fully probabilistic approach for the joint reconstruction of phylodynamic history in structured populations (such as geographic structure) based on a multitype birth–death process. This approach can be used to quantify the spread of a pathogen in a structured population. Changes in epidemic dynamics through time within subpopulations are incorporated through piecewise constant changes in transmission parameters.
We analyze a global human influenza H3N2 virus data set from a geographically structured host population to demonstrate how seasonal dynamics can be inferred simultaneously with the phylogeny and migration process. Our results suggest that the main migration path among the northern, tropical, and southern region represented in the sample analyzed here is the one leading from the tropics to the northern region. Furthermore, the time-dependent transmission dynamics between and within two HIV risk groups, heterosexuals and injecting drug users, in the Latvian HIV epidemic are investigated. Our analyses confirm that the Latvian HIV epidemic peaking around 2001 was mainly driven by the injecting drug user risk group.
Determining the timing of diversification of modern birds has been difficult. We combined DNA sequences of clock-like genes for most avian families with 130 fossil birds to generate a new time tree for Neornithes and investigated their biogeographic and diversification dynamics. We found that the most recent common ancestor of modern birds inhabited South America around 95 million years ago, but it was not until the Cretaceous-Paleogene transition (66 million years ago) that Neornithes began to diversify rapidly around the world. Birds used two main dispersion routes: reaching the Old World through North America, and reaching Australia and Zealandia through Antarctica. Net diversification rates increased during periods of global cooling, suggesting that fragmentation of tropical biomes stimulated speciation. Thus, we found pervasive evidence that avian evolution has been influenced by plate tectonics and environmental change, two basic features of Earth's dynamics.
Historical biogeography has been characterized by a large diversity of methods and unresolved debates about which processes, such as dispersal or vicariance, are most important for explaining distributions. A new R package, BioGeoBEARS, implements many models in a common likelihood framework, so that standard statistical model selection procedures can be applied to let the data choose the best model. Available models include a likelihood version of DIVA (“DIVALIKE”), LAGRANGE’s DEC model, and BAYAREA, as well as “+J” versions of these models which include founder-event speciation, an important process left out of most inference methods. I use BioGeoBEARS on a large sample of island and non-island clades (including two fossil clades) to show that founder-event speciation is a crucial process in almost every clade, and that most published datasets reject the non-J models currently in widespread use. BioGeoBEARS is open-source and freely available for installation at the Comprehensive R Archive Network at http://CRAN.R-project.org/package=BioGeoBEARS. A step-by-step tutorial is available at http://phylo.wikidot.com/biogeobears.
Bayesian total-evidence dating involves the simultaneous analysis of morphological data from the fossil record and morphological and sequence data from recent organisms, and it accommodates the uncertainty in the placement of fossils while dating the phylogenetic tree. Due to the flexibility of the Bayesian approach, total-evidence dating can also incorporate additional sources of information. Here, we take advantage of this and expand the analysis to include information about fossilization and sampling processes. Our work is based on the recently described fossilized birth-death (FBD) process, which has been used to model speciation, extinction and fossilization rates that can vary over time in a piecewise manner. So far, sampling of extant and fossil taxa has been assumed to be either complete or uniformly at random, an assumption which is only valid for a minority of datasets. We therefore extend the FBD process to accommodate diversified sampling of extant taxa, which is standard practice in studies of higher-level taxa. We verify the implementation using simulations and apply it to the early radiation of Hymenoptera (wasps, ants and bees). Previous total-evidence dating analyses of this dataset were based on a simple uniform tree prior and dated the initial radiation of extant Hymenoptera to the late Carboniferous (309 Ma). The analyses using the FBD prior under diversified sampling, however, date the radiation to the Triassic and Permian (252 Ma), slightly older than the age of the oldest hymenopteran fossils. By exploring a variety of FBD model assumptions, we show that it is mainly the accommodation of diversified sampling that causes the push towards more recent divergence times. Accounting for diversified sampling thus has the potential to close the long-discussed gap between rocks and clocks. We conclude that the explicit modeling of fossilization and sampling processes can improve divergence time estimates, but only if all important model aspects, including sampling biases, are adequately addressed.
Tropical Amphi-Pacific and trans-Pacific disjunctions are among the most controversial distribution patterns in biogeography. A disjunct distribution pattern between SE Asia (in fact, Indochina-Assam) and the Neotropics is rarely investigated in freshwater invertebrates. In the following, we give the first review on potential tropical Amphi-Pacific disjunctions in the Cladocera (Crustacea: Branchiopoda), a group of freshwater microcrustaceans. As a case study, we examine the littoral-benthic freshwater genus Leydigiopsis Sars, 1901 (Cladocera: Anomopoda: Chydoridae). The lineage has four known species in the Neotropics and we examine the status of Leydigiopsis records from Indochina and Assam (India). Our morphological study shows that the Oriental Leydigiopsis is not a human mediated introduced species from South America. The populations belong to a distinct species, which we describe as new from Thailand
and Vietnam. We discuss the biogeography of Leydigiopsis and examine possible hypotheses underlying the observed distribution pattern (e.g. transoceanic long-distance dispersal, boreotropical migration scenario, African extinction scenario). Our case study shows that a boreotropical origin seems the most plausible scenario for the current distribution of this tropical chydorid lineage. In the absence of a good fossil record, we propose that a comparison with biogeographical hypotheses of plants, may provide useful analogies when studying anomopod biogeography, because ephippia, the propagules for dispersal, functionally act as minute aquatic plant seeds. We list other examples of potential tropical Amphi-or trans-Pacific disjunctions in the Cladocera, based on phenotypes and we provide an updated key to the Leydigiopsis species of the world. Undersampling, taxonomical bias, the absence of molecular data and a poor fossil record, remain the most important obstacles for studying biogeography in non-planktonic tropical freshwater zooplankton.
We analysed patterns of animal dispersal, vicariance and diversification in the Holarctic based on complete phylogenies of 57 extant non-marine taxa, together comprising 770 species, documenting biogeographic events from the Late Mesozoic to the present. Four major areas, each corresponding to a historically persistent landmass, were used in the analyses: eastern Nearctic (EN), western Nearctic (WN), eastern Palaeoarctic (EP) and western Palaeoarctic (WP). Parsimony-based tree fitting showed that there is no significantly supported general area cladogram for the dataset. Yet, distributions are strongly phylogenetically conserved, as revealed by dispersal-vicariance analysis (DIVA). DIVA-based permutation tests were used to pinpoint phylogenetically determined biogeographic patterns. Consistent with expectations, continental dispersals (WP↓EP and WN↓EN) are significantly more common than palaeocontinental dispersals (WN↓EP and EN↓WP), which in turn are more common than disjunct dispersals (EN↓EP and WN↓WP). There is significant dispersal asymmetry both within the Nearctic (WN⇒EN more common than EN⇒WN) and the Palaeoarctic (EP⇒WP more common than WP⇒EP). Cross-Beringian faunal connections have traditionally been emphasized but are not more important than cross-Atlantic connections in our data set. To analyse changes over time, we sorted biogeographic events into four major time periods using fossil, biogeographic and molecular evidence combined with a «branching clock». These analyses show that trans-Atlantic distributions (EN–WP) were common in the Early–Mid Tertiary (70–20 Myr), whereas trans-Beringian distributions (WN–EP) were rare in that period. Most EN–EP disjunctions date back to the Early Tertiary (70–45 Myr), suggesting that they resulted from division of cross-Atlantic rather than cross-Beringian distributions. Diversification in WN and WP increased in the Quaternary (< 3 Myr), whereas in EP and EN it decreased from a maximum in the Early–Mid Tertiary.
Large phylogenomics data sets require fast tree inference methods, especially for maximum-likelihood (ML) phylogenies. Fast
programs exist, but due to inherent heuristics to find optimal trees, it is not clear whether the best tree is found. Thus,
there is need for additional approaches that employ different search strategies to find ML trees and that are at the same
time as fast as currently available ML programs. We show that a combination of hill-climbing approaches and a stochastic perturbation
method can be time-efficiently implemented. If we allow the same CPU time as RAxML and PhyML, then our software IQ-TREE found
higher likelihoods between 62.2% and 87.1% of the studied alignments, thus efficiently exploring the tree-space. If we use
the IQ-TREE stopping rule, RAxML and PhyML are faster in 75.7% and 47.1% of the DNA alignments and 42.2% and 100% of the protein
alignments, respectively. However, the range of obtaining higher likelihoods with IQ-TREE improves to 73.3–97.1%. IQ-TREE
is freely available at http://www.cibiv.at/software/iqtree.
A phylogenetic analysis of the two-clawed spiders grouped in Dionycha is presented, with 166 representative species of 49 araneomorph families, scored for 393 characters documented through standardized imaging protocols. The study includes 44 outgroup representatives of the main clades of Araneomorphae, and a revision of the main morphological character systems. Novel terminology is proposed for stereotyped structures on the chelicerae, and the main types of setae and silk spigots are reviewed, summarizing their characteristics. Clear homologs of posterior book lungs are described for early instars of Filistatidae, and a novel type of respiratory structure, the epigastric median tracheae, is described for some terminals probably related with Anyphaenidae or Eutichuridae. A new type of crypsis mechanism is described for a clade of thomisids, which in addition to retaining soil particles, grow fungi on their cuticle. Generalized patterns of cheliceral setae and macrosetae are proposed as synapomorphies of the Divided Cribellum and RTA clades. Dionycha is here proposed as a member of the Oval Calamistrum clade among the lycosoid lineages, and Liocranoides, with three claws and claw tufts, is obtained as a plausible sister group of the dionychan lineage. The morphology of the claw tuft and scopula is examined in detail and scored for 14 characters highly informative for relationships. A kind of seta intermediate between tenent and plumose setae (the pseudotenent type) is found in several spider families, more often reconstructed as a derivation from true tenent setae rather than as a phylogenetic intermediate. Corinnidae is retrieved in a restricted sense, including only the subfamilies Corinninae and Castianeirinae, while the ‘‘corinnid’’ genera retaining the median apophysis in the copulatory bulb are not clearly affiliated to any of the established families. Miturgidae is redefined, including Zoridae as a junior synonym. The Eutichuridae is raised to family status, as well as the Trachelidae and Phrurolithidae. New synapomorphies are provided for Sparassidae, Philodromidae, and Trachelidae. Philodromidae is presented as a plausible sister group of Salticidae, and these sister to Thomisidae; an alternative resolution placing thomisids in Lycosoidea is also examined. The Oblique Median Tapetum (OMT) clade is proposed for a large group of families including gnaphosoids, trachelids, liocranids, and phrurolithids, all having the posterior median eye tapeta forming a 90u angle, used for navigation by means of the polarized light in the sky as an optical compass; prodidomines seem to have further enhanced the mechanism by incorporating the posterior lateral eyes to the system. The Teutamus group is recognized for members of the OMT clade that are usually included in Liocranidae, but not closely related to Liocranum or phrurolithids. The Claw Tuft Clasper (CTC) clade is proposed for a group of families within the OMT clade, all having a peculiar mechanism grasping the folded base of the claw tuft setae with a hook on the superior claws. The CTC clade includes Trachelidae, Phrurolithidae, and several gnaphosoids such as Ammoxenidae, Cithaeronidae, Gnaphosidae, and Prodidomidae. A remarkable syndrome involving the expansion of the anterior lateral spinnerets, often sexually dimorphic, is here reported for some Miturgidae and several members of the CTC clade, in addition to the known cases in Clubionidae and ‘‘Liocranidae.’’ The following genera are transferred from Miturgidae to Eutichuridae: Calamoneta, Calamopus, Cheiracanthium, Cheiramiona, Ericaella, Eutichurus, Macerio, Radulphius, Strotarchus, Summacanthium, and Tecution; Lessertina is transferred from Corinnidae to Eutichuridae. The following genera are transferred to Miturgidae: Argoctenus, Elassoctenus, Hestimodema, Hoedillus, Israzorides, Odomasta, Simonus, Thasyraea, Tuxoctenus, Voraptus, Xenoctenus, Zora, and Zoroides, from Zoridae; Odo and Paravulsor, from Ctenidae; Pseudoceto from Corinnidae. The following genera are transferred from Corinnidae to Trachelidae: Afroceto, Cetonana, Fuchiba, Fuchibotulus, Meriola, Metatrachelas, Paccius, Paratrachelas, Patelloceto, Planochelas, Poachelas, Spinotrachelas, Thysanina, Trachelas, Trachelopachys, and Utivarachna. The following genera are transferred from Corinnidae to Phrurolithidae: Abdosetae, Drassinella, Liophrurillus, Plynnon, Orthobula, Otacilia, Phonotimpus, Phrurolinillus, Phrurolithus, Phruronellus, Phrurotimpus, Piabuna, and Scotinella. Dorymetaecus is transferred from Clubionidae to Phrurolithidae. Oedignatha and Koppe are transferred from Corinnidae to Liocranidae. Ciniflella is transferred from Amaurobiidae to Tengellidae.
Pantherine felids ('big cats') include the largest living cats, apex predators in their respective ecosystems. They are also the earliest diverging living cat lineage, and thus are important for understanding the evolution of all subsequent felid groups. Although the oldest pantherine fossils occur in Africa, molecular phylogenies point to Asia as their region of origin. This paradox cannot be reconciled using current knowledge, mainly because early big cat fossils are exceedingly rare and fragmentary. Here, we report the discovery of a fossil pantherine from the Tibetan Himalaya, with an age of Late Miocene-Early Pliocene, replacing African records as the oldest pantherine. A 'total evidence' phylogenetic analysis of pantherines indicates that the new cat is closely related to the snow leopard and exhibits intermediate characteristics on the evolutionary line to the largest cats. Historical biogeographic models provide robust support for the Asian origin of pantherines. The combined analyses indicate that 75% of the divergence events in the pantherine lineage extended back to the Miocene, up to 7 Myr earlier than previously estimated. The deeper evolutionary origin of big cats revealed by the new fossils and analyses indicate a close association between Tibetan Plateau uplift and diversification of the earliest living cats.
Historical biogeography seeks to understand the distribution of biodiversity in space and time. The dispersal-extinction-cladogenesis (DEC) model, a likelihood-based model of geographic range evolution, is widely used in assessing the biogeography of clades. Robust inference of dispersal and local extinction parameters is crucial for biogeographic inference, and yet a major caveat to its use is that the DEC model severely underestimates local extinction. We suggest that this is mainly due to the way in which the model is constructed to allow observed species to transition into being present in no areas (i.e., null range). By prohibiting transitions into the null range in the transition rate matrix, we were able to better infer local extinction and support this with simulations. This modified model, DEC*, has higher model fit and model adequacy than DEC, suggesting this modification should be considered for DEC and other models of geographic range evolution.
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 (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. However, analysis of the critique demonstrates a number of problems, ranging from mistakes in the example likelihood calculations through to misunderstanding the true causes of the likelihood advantage of DEC+J on typical datasets. I show that DEC+J fits better on datasets because the DEC model is statistically inadequate in the common situation when most species have geographic 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, I demonstrate that 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. 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.
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. Simulated data. Simulated data. 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. 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. 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.
In present work, we study six species of the genus Plator Simon, 1880 of the spider family Trochanteriidae Karsch, 1879, including five new species from China: Plator cyclicus sp. nov., P. dazhonghua sp. nov., P. hanyikani sp. nov., P. kamurai sp. nov. and P. qiului sp. nov. Plator sinicus Zhu & Wang, 1963 syn. nov. is regarded as a junior synonym of P. nipponicus (Kishida, 1914).
Six species, including two new species, of the spider genus Plator Simon 1880 belonging to the family Trochanteriidae from China are reviewed, which are Plator bowo sp. nov., P. insolens Simon 1880, P. pandeae Tikader 1969, P. pennatus Platnick, 1976, P. sinicus Zhu & Wang 1963 (revalidated) and P. yunlong sp. nov. The male of P. pennatus is described for the first time. Two species groups, Plator insolens group (including P. insolens, P. sinicus and the Japanese species P. nipponicus Kishida 1914) and Plator pennatus group (including P. bowo sp. nov., P. insolens, P. pandeae, P. pennatus and an Indian species, P. indicus Simon 1897) are recognized.
The boreotropics hypothesis postulates a preferential tropical biotic interchange between North America and Eurasia during the early Tertiary that was directed by Eocene thermal maxima and the close proximity of these two continental plates. This preferential interchange occurred at a time when South America was geologically and biotically isolated. A prediction of this hypothesis posits that a taxon with a present-day center of diversity in tropical North America, and with an early Tertiary fossil record from any region there, has a high probability of having sister-group relatives in the Paleotropics and derived relatives in South America. We propose a test of this prediction with phylogenetic studies of two pantropical taxa of Leguminosae that have early Tertiary North American fossil records. Our findings are consistent with the boreotropics hypothesis, and additional evidence suggests that many tropical elements in North America could be descendants of northern tropical progenitors. Ramifications of this hypothesis include the importance of integrating the fossil record with cladistic biogeographic studies, theoretical bases for recognizing tropical taxa with such disjunct distributions as Mexico and Madagascar, identification of taxa that may be most useful for testing vicariance models of Caribbean biogeography, and integrating the study of disjunct distributions in temperate regions of the northern hemisphere with those in the neo- and paleotropics.
Gnaphosidae Pocock are a very diverse spider family with remarkable spinning organ morphology. Although the family has received intense taxonomic attention in recent years, its intergeneric relationships remain obscure. A phylogenetic analysis of Gnaphosidae genera was performed to untangle the evolutionary history of the family. A matrix of 324 morphological characters, scored for 71 gnaphosid genera and 29 outgroup taxa, was analysed through parsimony and Bayesian phylogenetic inference. Gnaphosidae are not recovered as a monophyletic group, neither were most of the previously proposed intrafamiliar groupings. In accordance with the phylogenetic results obtained, Vectius Simon and Hemicloea Thorell are transferred to Trochanteriidae, and Xenoplectus Schiapelli & Gerschman de Pikelin to Liocranidae. Micaria Westring, Nauhea Forster and Verita Ramírez & Grismado (and some related genera) are probably not gnaphosids, although their phylogenetic placement is uncertain. Gnaphosidae s.s. are defined as spiders with enlarged piriform gland spigots, longer and wider than the major ampullate gland spigots. Within Gnaphosidae s.s., well-supported clades allow the redefinition, on the basis of quantitative phylogenetic evidence, of Gnaphosinae Pocock, Zelotinae Platnick, Herpyllinae Platnick, Drassodinae Simon, Prodidominae Simon rank res. and the newly proposed Leptodrassinae subfam. nov. Many genera are not assigned to subfamily given their poorly supported and unstable relationships. The homology and evolution of structures such as the claw tuft clasper, the spinning organs and the modification of cheliceral promargin are discussed.
Model-based molecular phylogenetics plays an important role in comparisons of genomic data, and model selection is a key step in all such analyses. We present ModelFinder, a fast model-selection method that greatly improves the accuracy of phylogenetic estimates by incorporating a model of rate heterogeneity across sites not previously considered in this context and by allowing concurrent searches of model space and tree space.
The phylogeny and evolutionary history of the whirligig beetle tribe Dineutini are inferred from the analysis of 56 morphological characters and DNA sequence data from the mitochondrial gene fragments COI, COII and 12S, and the nuclear gene fragments H3 and arginine kinase. Bayesian and maximum likelihood analyses were performed. A Bayesian tip-dating approach was taken to provide a time-calibrated phylogenetic tree incorporating fossil taxa. Seventy-one species of extant Gyrinidae were included in the analysis, as well as two fossil taxa, representing all dineutine genera and all proposed, nonmonotypic subgenera. The resulting trees strongly support the monophyly of the Dineutini and the genera Dineutus Macleay, 1825, Macrogyrus Régimbart, 1882, Porrorhynchus Laporte, 1835 and Enhydrus Laporte, 1835. The results do not support the distinction of Andogyrus Ochs, 1924 as a separate genus, nor do they support the majority of proposed subgenera. A new classification is presented here requiring the following taxonomic changes: Andogyrusstat. nov. is relegated to a subgenus of Macrogyrus; the following subgenera are synonymized with Macrogyruss.s.sensu nov.: Australogyrus Ochs, 1949 syn. nov., Ballogyrus Ochs, 1949 syn. nov., Clarkogyrus Ochs, 1949 syn. nov., Megalogyrus Ochs, 1949 syn. nov., Orectomimus Ochs, 1930 syn. nov. and Tribologyrus Ochs, 1949 syn nov.; the subgenus Stephanogyrus Ochs, 1955 syn. nov. is synonymized with the subgenus Cyclomimus Ochs, 1929; the genus Dineutus now includes two subgenera: Cyclous Dejean, 1833 sensu nov. and the Dineutuss.s. subgenus sensu nov.; the following subgenera are synonymized with the subgenus Cyclous: Callistodineutus Ochs, 1926 syn. nov., Paracyclous Ochs, 1926 syn. nov., Protodineutus Ochs, 1926 syn. nov. and Spinosodineutes Hatch, 1926 syn. nov.; and the following subgenera are synonymized with the Dineutuss.s. subgenus: Rhombodineutus Ochs, 1926 syn. nov. and Merodineutus Ochs, 1955 syn nov. The subgenus Rhomborhynchus Ochs, 1926 incert. sed. is tentatively moved to the genus Dineutus, without phylogenetic placement. The analysis confirms Mesodineutes† Ponomarenko, 1977 is a member of the Dineutini. Each genus and subgenus is reviewed in detail with (1) a morphological diagnosis, (2) its taxonomic circumscription, including the placement of species not included in the analysis, (3) known distribution and (4) relevant discussion. A new identification key to the extant genera and subgenera of the Dineutini is provided. Finally, a biogeographic analysis reconstructing ancestral ranges was conducted revealing the historical biogeography of the tribe. The historical biogeography of the Dineutini was found to be dominated primarily by dispersal, and we report a new transpacific disjunct distribution for members of the genus Dineutus.
Aim
Multiple biogeographical scenarios involving vicariance and different colonization routes can explain disjunct species distributions in the Southern Hemisphere. Here, we tested several alternative hypotheses in Eneopterinae crickets, a diverse subfamily presenting a disjunct worldwide distribution. We inferred a dated phylogeny of Eneopterinae and reconstructed their biogeographical history to unravel the origin of their present‐day distribution, focusing on their multiple origins in the Neotropics.
Location
Worldwide.
Methods
We sampled 62 eneopterine species representing all extant genera. We inferred their phylogenetic relationships through Bayesian and maximum likelihood approaches based on four mitochondrial and three nuclear gene sequences. Divergence time estimates were inferred using Bayesian relaxed clock approaches and primary fossil calibrations. Biogeographical analyses were conducted with the default dispersal–extinction–cladogenesis ( DEC ) model and a variant model ( DEC +J), which accounts for rare‐jump dispersal events.
Results
Our dating analyses showed that the Eneopterinae is far older than expected and its diversification can be traced back to the Late Cretaceous ( c . 76 Ma). In this context, the most supported biogeographical scenario (under DEC +J) suggests that the Neotropics were colonized twice independently: first during the break‐up of Gondwana, when Antarctica, Australia and South America started separating (compatible with a vicariance event if relying on the result of the DEC model alone); later through a northern recolonization originating from Southeast Asia, likely related to a Holarctic Boreotropical distribution of an eneopterine lineage during the Eocene.
Main conclusions
We provided a dated worldwide biogeographical framework for the Eneopterinae crickets. Overall, the subfamily disjunct distribution pattern is better explained by both ancient and recent dispersal events. Whether this could reflect a widespread pattern in insect groups exhibiting a disjunct distribution remains to be investigated by studying other insect lineages. The information gathered here will also help foster new directions for future studies concerning the acoustic innovations of this clade.
Arachnida is an ancient, diverse, and ecologically important animal group that contains a number of species of interest for medical, agricultural, and engineering applications. Despite their importance, many aspects of the arachnid tree of life remain unresolved, hindering comparative approaches to arachnid biology. Biologists have made considerable efforts to resolve the arachnid phylogeny; yet, limited and challenging morphological characters, as well as a dearth of genetic resources, have hindered progress. Here, we present a genomic toolkit for arachnids featuring hundreds of conserved DNA regions (ultraconserved elements or UCEs) that allow targeted sequencing of any species in the arachnid tree of life. We used recently developed capture probes designed from conserved regions of available arachnid genomes to enrich a sample of loci from 32 diverse arachnids. Sequence capture returned an average of 487 UCE loci for all species, with a range from 170 to 722. Phylogenetic analysis of these UCEs produced a highly resolved arachnid tree with relationships largely consistent with recent transcriptome-based phylogenies. We also tested the phylogenetic informativeness of UCE probes within the spider, scorpion, and harvestman orders, demonstrating the utility of these markers at shallower taxonomic scales, and suggesting that these loci will be useful for species-level differences. This probe set will open the door to phylogenomic and population genomic studies across the arachnid tree of life, enabling systematics, species delimitation, species discovery, and conservation of these diverse arthropods. This article is protected by copyright. All rights reserved.
Six species, including two new species, of the spider genus Plator Simon 1880 belonging to the family Trochanteriidae from China are reviewed, which are Plator bowo sp. nov., P. insolens Simon 1880, P. pandeae Tikader 1969, P. pennatus Platnick, 1976, P. sinicus Zhu & Wang 1963 (revalidated) and P. yunlong sp. nov. The male of P. pennatus is described for the first time. Two species groups, Plator insolens group (including P. insolens, P. sinicus and the Japanese species P. nipponicus Kishida 1914) and Plator pennatus group (including P. bowo sp. nov., P. insolens, P. pandeae, P. pennatus and an Indian species, P. indicus Simon 1897) are recognized.
Four main potential contributions of fossils to phylogenetic systematics and historical biogeography are (1) to provide additional taxa which (when sufficiently well preserved) can give new morphological and ontogenetic data in addition to those provided by Recent species; (2) to provide additional taxa which can increase the known biogeographic range of a taxon; (3) to help establish a minimum age for a taxon; and (4) to present fossil biotas that can be examined for biogeographic patterns not recognizable in younger (including the Recent) or older biotas.
The first three points have been expressed or at least implied by other workers and are only briefly reviewed. The fourth point is proposed as a method of using fossil biotas to provide time controls to cladistic studies of historical biogeography. Previously, cladistic vicariance biogeographers have used fossil plus Recent biotas, or the Recent biota alone, for the geographic areas of study. Such investigations that lack any time control in the data base cannot effectively deal with areas that have complex histories as, for example, an earlier area of endemism in which area relationships are later complicated through the addition of exotic taxa by dispersal. By using time controls provided by fossil biotas, we may learn more about the relationships of areas with complex histories and may reveal biogeographical information that is sometimes unavailable through examination of the Recent biota.
The 1980 eruption of Mount St. Helens created a large area (the Pumice Plain) which initially lacked any resident arthropods. From 1981-1986, ballooning spiders made up over 23% of windblown arthropod fallout and contributed 105 individuals per m2 (91 mg dry biomass) over 1 summer. The family Lycosidae included 49% of all specimens but only 9% of all species; Linyphiidae included 34% of specimens and 50% of species. The 125 spider species taken varied widely in ballooning phenology. By 1986, six species (the lycosids Pardosa wyuta and P. lowriei and the linyphiids Erigone dentosa, E. aletris, E. capra and Walckenaeria pellax) had established reproducing populations on the Pumice Plain, almost entirely at sites already colonized by vegetation. Successful colonists showed distinct phenological patterns (compared to subpopulations composed entirely of immigrants) and, in Pardosa, direct evidence of reproduction (egg sacs and progeny). Most incoming spiders were apparently unable to reproduce on the Pumice Plain, which thus became a reproductive sink for their taxa. Aerial dispersal is of prime importance in recolonization of devastated terrain, and its extent in other situations has been underestimated.
Palynological data emphasize the presence of two distinctive provinces during the Late Cretaceous, one including eastern North America and Europe and a second including the major part of Asia and western North America. The distinction between these two provinces became increasingly blurred during the Paleogene. During the Eocene, the ram forests of both Europe and western North America shared numerous genera, both extinct and extant. The great majority of the latter and most of the closest extant relatives of the former now occur in the Indomalayan region. It is thus clear that much of the present Indomalayan flora represents a relict of a once widespread Northern Hemisphere tropical (s.l.) flora, one that has largely (but not entirely) been eliminated from the New World. Among the possible New World survivors of this boreotropical flora are some of the dry Caribbean genera, which could have been derived from lineages of the dry tropical vegetation of the Gulf Coast Eocene; only a handful of present Neotropical lowland rain forest genera appear to be boreotropical relicts.
In a 1935 paper and in his book Theory of Probability, Jeffreys developed a methodology for quantifying the evidence in favor of a scientific theory. The centerpiece was a number, now called the Bayes factor, which is the posterior odds of the null hypothesis when the prior probability on the null is one-half. Although there has been much discussion of Bayesian hypothesis testing in the context of criticism of P-values, less attention has been given to the Bayes factor as a practical tool of applied statistics. In this article we review and discuss the uses of Bayes factors in the context of five scientific applications in genetics, sports, ecology, sociology, and psychology. We emphasize the following points:
Significance
Divergence time estimation on an absolute timescale requires external calibration information, which typically is derived from the fossil record. The common practice in Bayesian divergence time estimation involves applying calibration densities to individual nodes. Often, these priors are arbitrarily chosen and specified yet have an excessive impact on estimates of absolute time. We introduce the fossilized birth–death process—a fossil calibration method that unifies extinct and extant species with a single macroevolutionary model, eliminating the need for ad hoc calibration priors. Compared with common calibration density approaches, Bayesian inference under this mechanistic model yields more accurate node age estimates while providing a coherent measure of statistical uncertainty. Furthermore, unlike calibration densities, our model accommodates all the reliable fossils for a given phylogenetic dataset.
The phylogenetic relationships of some Neotropical plant groups have proved to be different from expectation assuming plate tectonics as the underlying model, and these unanticipated relationships (and their timing) have required further work to explain how they came into existence. Well‐known Neotropical families, such as Bromeliaceae and Cactaceae, have one to a few species in Africa, but these can be explained by recent long‐distance dispersals; the estimated ages of the Transatlantic crown and stem clades of these families are of relatively recent origin, so long‐distance dispersal is the only possible explanation and plate tectonic explanations are not viable. Other families with a crown age appropriate to be explained by plate tectonics did not seem to have distributions indicating an involvement of long‐distance dispersal, but the advent of molecular systematics and molecular clocks has shown this to be otherwise. Families exhibiting this pattern include Fabaceae and Lauraceae (and many others), and in spite of the unlikely dispersal qualities of their generally large seeds, they exhibit many instances of long‐distance dispersal occurring throughout their evolutionary history; in fact, long‐distance dispersal is the most probable explanation to account for the current distributions of the great majority of land plant families. One factor that sometimes is overlooked is the boreotropics hypothesis, which may explain more recent connections between American, African and Asian floristic components. However, in some old lineages with small propagules that appear well adapted to long‐distance dispersal, such as Marattiaceae and Orchidaceae, we find a pattern suggesting that tectonics is the primary factor, with clades clearly restricted to one tropical region. These patterns appear to have little to do with dispersability and it is probable that their conforming to expected (tectonic) biogeographical patterns has to do with their specialized life‐history strategies that have acted to make intercontinental establishment unlikely even though dispersal almost certainly occurs. Molecular studies have identified additional, unanticipated clades, and these fit into the relictual category with what may be an overlay of old long‐distance dispersal events. Examples at the ordinal level are Crossosomatales and Huerteales, and we expect future studies to identify more of these relict and unexpected clades at many taxonomic levels. Overall, molecular systematic studies and molecular clocks have demonstrated that there are many more connections between the Neotropics and Palaeotropics, both Asia and Africa, than previously would have been thought under a plate tectonic model. © 2012 The Linnean Society of London, Botanical Journal of the Linnean Society, 2012,, –.
2013.01 Abstract: The tectonic evolution of the Indian Plate, which started in Late Jurassic about 167 million years ago (approximately 167Ma) with the breakup of Gondwana, presents an exceptional and intricate case history against which a variety of plate tectonic events such as: continental breakup, sea-floor spreading, birth of new oceans, flood basalt volcanism, hotspot tracks, transform faults, subduction, obduction, continental collision, accretion, and mountain building can be investigated. Plate tectonic maps are presented here illustrating the repeated rifting of the Indian plate from surrounding Gondwana continents, its northward migration, and its collision first with the Kohistan-Ladakh Arc at the Indus Suture Zone, and then with Tibet at the Shyok -Tsangpo Suture. The associations between flood basalts and the recurrent separation of the Indian plate from Gondwana are assessed. The breakup of India from Gondwana and the opening of the Indian Ocean is thought to have been caused by plate tectonic forces which were localized along zones of weakness caused by mantle plumes (Bouvet, Marion, Kerguelen, and Reunion Plumes). The sequential spreading of the Southwest Indian Ridge/Davie Ridge, Southeast Indian Ridge, Central Indian Ridge, Palitana Ridge, and Carlsberg Ridge in the Indian Ocean were responsible for the fragmentation of the Indian Plate during the Late Jurassic and Cretaceous times. The Reunion and the Kerguelen Plumes left two spectacular hotspot tracks on either side of the Indian Plate. With the breakup of Gondwana, India remained isolated as an island continent, but reestablished its biotic links with Africa during the Late Cretaceous during its collision with the Kohistan-Ladakh Arc ( approximately 85Ma) along the Indus Suture. Soon after the Deccan eruption, India drifted northward as an island continent by rapid motion carrying Gondwana biota, about 20cm/year, between 67Ma to 50Ma; it slowed down dramatically to 5cm/year during its collision with Asia in early Eocene ( approximately 50Ma). A northern corridor was established between India and Asia soon after the collision allowing faunal interchange.
This is reflected by mixed Gondwana and Eurasian elements in the fossil record preserved in several continental Eocene formations of India. A revised India-Asia collision model suggests that the Indus Suture represents the obduction zone between India and the Kohistan-Ladakh Arc, whereas the Shyok Suture represents the collision between the Kohistan-Ladakh Arc and Tibet. Eventually, the Indus-Tsangpo Zone became the locus of the final India-Asia collision, which probably began in early Eocene ( approximately 50Ma) with the closure of Neotethys Ocean. The post-collisional tectonics for the last 50 million years is best expressed in the evolution of the Himalaya-Tibetan Orogen. The great thickness of crust beneath Tibet and Himalaya and a series of north vergent thrust zones in the Himalaya and the south-vergent subduction zones in Tibetan Plateau suggest the progressive convergence between India and Asia of about 2500km since the time of collision. In the early Eohimalayan phase ( approximately 50 to 25Ma) of Himalayan Orogeny (middle Eocene-late Oligocene), thick sediments on the leading edge of the Indian Plate were squeezed, folded, and faulted to form the Tethyan Himalaya. With continuing convergence of India, the architecture of the Himalayan - Tibetan Orogen is dominated by deformational structures developed in the Neogene Period during the Neohimalayan phase ( approximately 21Ma to present), creating a series of north-vergent thrust belt systems such as the Main Central Thrust, the Main Boundary Thrust, and the Main Frontal Thrust to accommodate crustal shortening. Neogene molassic sediment shed from the rise of the Himalaya was deposited in a nearly continuous foreland trough in the Siwalik Group containing rich vertebrate assemblages. Tomographic imaging of the India-Asia Orogen reveals that Indian lithospheric slab has been subducted subhorizontally beneath the entire Tibetan Plateau that has played a key role in the uplift of the Tibetan Plateau. The low-viscosity channel flow in response to topographic loading of Tibet provides a mechanism to explain the Himalayan-Tibetan Orogen. From the start of its voyage in Southern Hemisphere, to its final impact with the Asia, the Indian Plate has experienced changes in climatic conditions both short-term and long-term. We present a series of
paleoclimatic maps illustrating the temperature and precipitation conditions based on estimates of Fast Ocean Atmospheric Model, a coupled global climate model. The uplift of the Himalaya-Tibetan Plateau above the snow line created two most important global climate phenomena-the birth of the Asian monsoon and the onset of Pleistocene glaciation. As the mountains rose, and the monsoon rains intensified, increasing erosional sediments from the Himalaya were carried down by the Ganga River in the east and the Indus River in the west, and were deposited in two great deep-sea fans, the Bengal and the Indus. Vertebrate fossils provide additional resolution for the timing of three crucial tectonic events: India-KL Arc collision during the Late Cretaceous, India-Asia collision during the early Eocene, and the rise of the Himalaya during the early Miocene.