scholarly journals Fossil biogeography: a new model to infer dispersal, extinction and sampling from palaeontological data

2016 ◽  
Vol 371 (1691) ◽  
pp. 20150225 ◽  
Author(s):  
Daniele Silvestro ◽  
Alexander Zizka ◽  
Christine D. Bacon ◽  
Borja Cascales-Miñana ◽  
Nicolas Salamin ◽  
...  
Keyword(s):  
North America ◽  
Fossil Record ◽  
Phylogenetic Trees ◽  
Phylogenetic Analyses ◽  
Historical Biogeography ◽  
Extinction Rates ◽  
Climatic Cooling ◽  
Fossil Data ◽  
Incomplete Sampling ◽  
Des Model

Methods in historical biogeography have revolutionized our ability to infer the evolution of ancestral geographical ranges from phylogenies of extant taxa, the rates of dispersals, and biotic connectivity among areas. However, extant taxa are likely to provide limited and potentially biased information about past biogeographic processes, due to extinction, asymmetrical dispersals and variable connectivity among areas. Fossil data hold considerable information about past distribution of lineages, but suffer from largely incomplete sampling. Here we present a new dispersal–extinction–sampling (DES) model, which estimates biogeographic parameters using fossil occurrences instead of phylogenetic trees. The model estimates dispersal and extinction rates while explicitly accounting for the incompleteness of the fossil record. Rates can vary between areas and through time, thus providing the opportunity to assess complex scenarios of biogeographic evolution. We implement the DES model in a Bayesian framework and demonstrate through simulations that it can accurately infer all the relevant parameters. We demonstrate the use of our model by analysing the Cenozoic fossil record of land plants and inferring dispersal and extinction rates across Eurasia and North America. Our results show that biogeographic range evolution is not a time-homogeneous process, as assumed in most phylogenetic analyses, but varies through time and between areas. In our empirical assessment, this is shown by the striking predominance of plant dispersals from Eurasia into North America during the Eocene climatic cooling, followed by a shift in the opposite direction, and finally, a balance in biotic interchange since the middle Miocene. We conclude by discussing the potential of fossil-based analyses to test biogeographic hypotheses and improve phylogenetic methods in historical biogeography.

Evolution and the fossil record: patterns, rates, and processes

1987 ◽  
Vol 65 (5) ◽  
pp. 1053-1060 ◽  
Author(s):  
Philip D. Gingerich
Keyword(s):  
Fossil Record ◽  
Evolutionary Rates ◽  
Short Intervals ◽  
Evolutionary Diversification ◽  
Extinction Rates ◽  
Local Areas ◽  
Climatic Cooling ◽  
Intensive Sampling ◽  
Underlying Processes ◽  
Morphological Innovation

Mammals have an unusually good Cenozoic fossil record providing evidence of their evolutionary diversification. We view this record in hindsight, which biases our perception in many ways. Overall worldwide diversity appears to increase exponentially through time, while intensive sampling in local areas indicates that modern levels of diversity were achieved early in the Cenozoic. The evident significance of Pleistocene extinctions depends critically on how extinction rates are quantified. Our taxonomic hierarchy probably reflects the number of major faunal turnovers a group has survived rather than declining intensity of successive turnovers. Morphological innovation and taxonomic diversification appear following intervals of climatic cooling, suggesting that major features of evolution are extrinsically controlled. Favorable stratigraphic settings yield detailed records of gradual anagenesis and cladogenesis in mammals, with intermediates present as evidence of transition. The apparent dichotomy between high evolutionary rates measured by neontologists over short intervals of time and low evolutionary rates measured by paleontologists over long intervals of time disappears when rates are measured on intermediate scales of time. Microevolution and macroevolution are manifestations of common underlying processes expressed on different time scales.

scholarly journals Historical biogeography of two cosmopolitan families of flowering plants: Annonaceae and Rhamnaceae

2004 ◽  
Vol 359 (1450) ◽  
pp. 1495-1508 ◽  
Author(s):  
J. E. Richardson ◽  
L. W. Chatrou ◽  
J. B. Mols ◽  
R. H. J. Erkens ◽  
M. D. Pirie
Keyword(s):  
Dna Sequences ◽  
Phylogenetic Trees ◽  
Phylogenetic Analyses ◽  
Plastid Dna ◽  
Distribution Patterns ◽  
Historical Biogeography ◽  
Rate Heterogeneity ◽  
Long Distance ◽  
Fossil Calibration ◽  
Dispersal Capability

Annonaceae are a pantropically distributed family found predominantly in rainforests, so they are megathermal taxa, whereas Rhamnaceae are a cosmopolitan family that tend to be found in xeric regions and may be classified as mesothermal. Phylogenetic analyses of these families are presented based on rbcL and trn L–F plastid DNA sequences. Likelihood ratio tests revealed rate heterogeneity in both phylogenetic trees and they were therefore made ultrametric using non–parametric rate smoothing and penalized likelihood. Divergence times were then estimated using fossil calibration points. The historical biogeography of these families that are species rich in different biomes is discussed and compared with other published reconstructions. Rhamnaceae and most lineages within Annonaceae are too young to have had their distribution patterns influenced by break–up of previously connected Gondwanan landmasses. Contrasts in the degree of geographical structure between these two families may be explained by differences in age and dispersal capability. In both groups, long–distance dispersal appears to have played a more significant role in establishing modern patterns than had previously been assumed. Both families also contain examples of recent diversification of species–rich lineages. An understanding of the processes responsible for shaping the distribution patterns of these families has contributed to our understanding of the historical assembly of the biomes that they occupy.

Assessing the effect of time-scaling methods on phylogeny-based analyses in the fossil record

Paleobiology ◽  
10.1666/13033 ◽  
2014 ◽  
Vol 40 (3) ◽  
pp. 331-351 ◽  
Author(s):  
David W. Bapst
Keyword(s):  
Fossil Record ◽  
Scaling Method ◽  
Short Branch ◽  
Time Scaling ◽  
Temporal Relationships ◽  
Branch Lengths ◽  
Scaling Methods ◽  
True Time ◽  
Fossil Data ◽  
Incomplete Sampling

Phylogeny-based approaches can be used to infer diversification dynamics and the rate and pattern of trait change. Applying these analyses to fossil data often requires time-scaling a cladogram of morphotaxon relationships. Although several time-scaling methods have been developed for this purpose, the incomplete sampling of the fossil record can distort the apparent timing of branching. It is unclear how well different time-scaling methods reconstruct the true temporal relationships or how any such inaccuracy could affect tree-based evolutionary analyses. I developed process-based simulations of the fossil record that allow the comparison of approximated time-scaled trees to true time-scaled trees. I used this simulation framework to test the effect of time-scaling methods on the fidelity of several commonly applied tree-based analyses, across a range of simulation conditions. When the fidelity of time-scaling methods differed, the stochastic “cal3”time-scaling method with ancestral assignment produced preferable results. Estimating rates and models of continuous trait evolution was particularly sensitive to bias from scenarios that forced the insertion of many short branch lengths, a bias that is not solved by any of the considered time-scaling methods in all scenarios. Thecal3method of time-scaling can be recommended as the preferred time-scaling method among those tested, but caution must be exercised because tree-based analyses are prone to easily overlooked biases.

scholarly journals Emergence of hystricognathous rodents: Palaeogene fossil record, phylogeny, dental evolution and historical biogeography

2019 ◽  
Vol 187 (3) ◽  
pp. 929-964 ◽  
Author(s):  
Laurent Marivaux ◽  
Myriam Boivin
Keyword(s):  
South America ◽  
Fossil Record ◽  
Phylogenetic Trees ◽  
Middle Eocene ◽  
Historical Biogeography ◽  
South American ◽  
Dental Evolution ◽  
Dental Evidence ◽  
Dispersal Events ◽  
Masticatory Apparatus

AbstractAlthough phylogenetic trees imply Asia as the ancestral homeland of the Hystricognathi clade (Rodentia: Ctenohystrica), curiously the oldest known fossil occurrences of hystricognathous rodents are not from Asia, but from Africa and South America, where they appear suddenly in the fossil record of both landmasses by the Late Middle Eocene. Here we performed cladistic and Bayesian (standard and tip-dating analyses) assessments of the dental evidence documenting early ctenohystricans, including several Asian ‘ctenodactyloids’, virtually all Palaeogene Asian and African hystricognaths known thus far and two representatives of the earliest known South American hystricognaths. Our results provide a phylogenetic context of early hystricognaths (with implications on systematics) and suggest that some Eocene Asian ‘ctenodactyloids’ could be considered as stem hystricognaths and pre-hystricognaths, although they were not recognized as such originally. However, this view does not fill the gap of the Eocene Asian hystricognath record, as the proposed results imply many ghost lineages extending back to the Middle Eocene for several Asian and African taxa. They also imply a complex early historical biogeography of the group, involving multiple dispersal events from Asia to Africa (and possibly from Africa back to Asia) and then to South America sometime during the Middle Eocene. Based on these phylogenetic considerations, we discuss the emergence of hystricognathous rodents from a morpho-anatomical perspective by analysing the differentiation of their masticatory apparatus and chewing movements, notably through the evolution of their dental patterns.

scholarly journals Continental faunal exchange and the asymmetrical radiation of carnivores

2015 ◽  
Vol 282 (1817) ◽  
pp. 20151952 ◽  
Author(s):  
Mathias M. Pires ◽  
Daniele Silvestro ◽  
Tiago B. Quental
Keyword(s):  
Climate Change ◽  
North America ◽  
Biological Invasions ◽  
Bayesian Approach ◽  
Fossil Record ◽  
Long Term Outcomes ◽  
Extinction Rates ◽  
Asymmetrical Pattern ◽  
Evolutionary Radiations

Lineages arriving on islands may undergo explosive evolutionary radiations owing to the wealth of ecological opportunities. Although studies on insular taxa have improved our understanding of macroevolutionary phenomena, we know little about the macroevolutionary dynamics of continental exchanges. Here we study the evolution of eight Carnivora families that have migrated across the Northern Hemisphere to investigate if continental invasions also result in explosive diversification dynamics. We used a Bayesian approach to estimate speciation and extinction rates from a substantial dataset of fossil occurrences while accounting for the incompleteness of the fossil record. Our analyses revealed a strongly asymmetrical pattern in which North American lineages invading Eurasia underwent explosive radiations, whereas lineages invading North America maintained uniform diversification dynamics. These invasions into Eurasia were characterized by high rates of speciation and extinction. The radiation of the arriving lineages in Eurasia coincide with the decline of established lineages or phases of climate change, suggesting differences in the ecological settings between the continents may be responsible for the disparity in diversification dynamics. These results reveal long-term outcomes of biological invasions and show that the importance of explosive radiations in shaping diversity extends beyond insular systems and have significant impact at continental scales.

scholarly journals Bayesian estimation of fossil phylogenies and the evolution of early to middle Paleozoic crinoids (Echinodermata)

2017 ◽  
Vol 91 (4) ◽  
pp. 799-814 ◽  
Author(s):  
David F. Wright
Keyword(s):  
Phylogenetic Relationships ◽  
Fossil Record ◽  
Phylogenetic Trees ◽  
Probabilistic Models ◽  
Sister Group ◽  
Deep Time ◽  
Recent Developments ◽  
Middle Paleozoic ◽  
Phylogenetic Affinities ◽  
Fossil Data

AbstractKnowledge of phylogenetic relationships among species is fundamental to understanding basic patterns in evolution and underpins nearly all research programs in biology and paleontology. However, most methods of phylogenetic inference typically used by paleontologists do not accommodate the idiosyncrasies of fossil data and therefore do not take full advantage of the information provided by the fossil record. The advent of Bayesian ‘tip-dating’ approaches to phylogeny estimation is especially promising for paleosystematists because time-stamped comparative data can be combined with probabilistic models tailored to accommodate the study of fossil taxa. Under a Bayesian framework, the recently developed fossilized birth–death (FBD) process provides a more realistic tree prior model for paleontological data that accounts for macroevolutionary dynamics, preservation, and sampling when inferring phylogenetic trees containing fossils. In addition, the FBD tree prior allows for the possibility of sampling ancestral morphotaxa. Although paleontologists are increasingly embracing probabilistic phylogenetic methods, these recent developments have not previously been applied to the deep-time invertebrate fossil record. Here, I examine phylogenetic relationships among Ordovician through Devonian crinoids using a Bayesian tip-dating approach. Results support several clades recognized in previous analyses sampling only Ordovician taxa, but also reveal instances where phylogenetic affinities are more complex and extensive revisions are necessary, particularly among the Cladida. The name Porocrinoidea is proposed for a well-supported clade of Ordovician ‘cyathocrine’ cladids and hybocrinids. The Eucladida is proposed as a clade name for the sister group of the Flexibilia herein comprised of cladids variously considered ‘cyathocrines,’ ‘dendrocrines,’ and/or ‘poteriocrines’ by other authors.

Darwin's two competing phylogenetic trees: marsupials as ancestors or sister taxa?

2012 ◽  
Vol 39 (2) ◽  
pp. 217-233 ◽  
Author(s):  
J. David Archibald
Keyword(s):  
Fossil Record ◽  
Evolutionary Biology ◽  
Phylogenetic Trees ◽  
Charles Darwin ◽  
The Other ◽  
Charles Lyell ◽  
Single Origin ◽  
Molecular Studies ◽  
Richard Owen ◽  
First Time

Studies of the origin and diversification of major groups of plants and animals are contentious topics in current evolutionary biology. This includes the study of the timing and relationships of the two major clades of extant mammals – marsupials and placentals. Molecular studies concerned with marsupial and placental origin and diversification can be at odds with the fossil record. Such studies are, however, not a recent phenomenon. Over 150 years ago Charles Darwin weighed two alternative views on the origin of marsupials and placentals. Less than a year after the publication of On the origin of species, Darwin outlined these in a letter to Charles Lyell dated 23 September 1860. The letter concluded with two competing phylogenetic diagrams. One showed marsupials as ancestral to both living marsupials and placentals, whereas the other showed a non-marsupial, non-placental as being ancestral to both living marsupials and placentals. These two diagrams are published here for the first time. These are the only such competing phylogenetic diagrams that Darwin is known to have produced. In addition to examining the question of mammalian origins in this letter and in other manuscript notes discussed here, Darwin confronted the broader issue as to whether major groups of animals had a single origin (monophyly) or were the result of “continuous creation” as advocated for some groups by Richard Owen. Charles Lyell had held similar views to those of Owen, but it is clear from correspondence with Darwin that he was beginning to accept the idea of monophyly of major groups.

scholarly journals Predicting the Impact of Describing New Species on Phylogenetic Patterns

2019 ◽  
Vol 1 (1) ◽  
Author(s):  
D C Blackburn ◽  
G Giribet ◽  
D E Soltis ◽  
E L Stanley
Keyword(s):  
New Species ◽  
Phylogenetic Trees ◽  
Branch Length ◽  
Length Variation ◽  
Tree Shape ◽  
Branch Lengths ◽  
Taxonomic History ◽  
Ecological Patterns ◽  
The Impact ◽  
Incomplete Sampling

Abstract Although our inventory of Earth’s biodiversity remains incomplete, we still require analyses using the Tree of Life to understand evolutionary and ecological patterns. Because incomplete sampling may bias our inferences, we must evaluate how future additions of newly discovered species might impact analyses performed today. We describe an approach that uses taxonomic history and phylogenetic trees to characterize the impact of past species discoveries on phylogenetic knowledge using patterns of branch-length variation, tree shape, and phylogenetic diversity. This provides a framework for assessing the relative completeness of taxonomic knowledge of lineages within a phylogeny. To demonstrate this approach, we use recent large phylogenies for amphibians, reptiles, flowering plants, and invertebrates. Well-known clades exhibit a decline in the mean and range of branch lengths that are added each year as new species are described. With increased taxonomic knowledge over time, deep lineages of well-known clades become known such that most recently described new species are added close to the tips of the tree, reflecting changing tree shape over the course of taxonomic history. The same analyses reveal other clades to be candidates for future discoveries that could dramatically impact our phylogenetic knowledge. Our work reveals that species are often added non-randomly to the phylogeny over multiyear time-scales in a predictable pattern of taxonomic maturation. Our results suggest that we can make informed predictions about how new species will be added across the phylogeny of a given clade, thus providing a framework for accommodating unsampled undescribed species in evolutionary analyses.

Anatomical, morphometric, and stratigraphic analyses of theropod biodiversity in the Upper Cretaceous (Campanian) Dinosaur Park Formation

2021 ◽  
pp. 1-15
Author(s):  
Thomas M. Cullen ◽  
Lindsay Zanno ◽  
Derek W. Larson ◽  
Erinn Todd ◽  
Philip J. Currie ◽  
...  
Keyword(s):  
High Resolution ◽  
North America ◽  
Fossil Record ◽  
Upper Cretaceous ◽  
Environmental Changes ◽  
Morphometric Analyses ◽  
Variable Distribution ◽  
Taxic Diversity ◽  
Dinosaur Park Formation ◽  
Broad Scale

The Dinosaur Park Formation (DPF) of Alberta, Canada, has produced one of the most diverse dinosaur faunas, with the record favouring large-bodied taxa, in terms of number and completeness of skeletons. Although small theropods are well documented in the assemblage, taxonomic assessments are frequently based on isolated, fragmentary skeletal elements. Here we reassess DPF theropod biodiversity using morphological comparisons, high-resolution biostratigraphy, and morphometric analyses, with a focus on specimens/taxa originally described from isolated material. In addition to clarifying taxic diversity, we test whether DPF theropods preserve faunal zonation/turnover patterns similar to those previously documented for megaherbivores. Frontal bones referred to a therizinosaur (cf. Erlikosaurus), representing among the only skeletal record of the group from the Campanian–Maastrichtian (83–66 Ma) fossil record of North America, plot most closely to troodontids in morphospace, distinct from non-DPF therizinosaurs, a placement supported by a suite of troodontid anatomical frontal characters. Postcranial material referred to cf. Erlikosaurus in North America is also reviewed and found most similar in morphology to caenagnathids, rather than therizinosaurs. Among troodontids, we document considerable morphospace and biostratigraphic overlap between Stenonychosaurus and the recently described Latenivenatrix, as well as a variable distribution of putatively autapomorphic characters, calling the validity of the latter taxon into question. Biostratigraphically, there are no broad-scale patterns of faunal zonation similar to those previously documented in ornithischians from the DPF, with many theropods ranging throughout much of the formation and overlapping extensively, possibly reflecting a lack of sensitivity to environmental changes, or other cryptic ecological or evolutionary factors.

A review of gall midges (Diptera: Cecidomyiidae) described from Mesozoic deposits

2021 ◽  
Vol 4 (1) ◽  
pp. 001-014
Author(s):  
MATHIAS JASCHHOF
Keyword(s):  
New Zealand ◽  
North America ◽  
Fossil Record ◽  
Morphological Diversity ◽  
Sensu Stricto ◽  
Junior Synonym ◽  
Gall Midges ◽  
Incertae Sedis ◽  
New Tribe

Twenty-four fossil gall midges (Cecidomyiidae) described from 1917–2020 from Mesozoic deposits, mostly ambers, are reviewed. Information from the original publications is used as the basis for reinterpretation, when such is regarded as appropriate here. As a result, the fossil record of cecidomyiids from the Mesozoic comprises representatives of the following subfamilies and tribes, all mycophagous (numbers in parentheses refer to species described): Catotrichinae (1); Micromyinae: Catochini (2), Amediini (1), Campylomyzini (1), Micromyini (2) and Aprionini (1); Winnertziinae: Heteropezini (2), Diallactiini (4) and Winnertziini (1); Porricondylinae: Dicerurini (1). Other Winnertziinae (3) and Micromyinae (5) cannot be classified to tribe because information on critical morphological structures is unavailable; they are thus considered incertae sedis. Members of the Lestremiinae sensu stricto are unrecorded from the Mesozoic, as are any Cecidomyiinae (the only subfamily containing phytophages and predators). Commonly occurring reasons for misinterpretation of amber fossils are the non-recognition of artefacts and the unfamiliarity with group-specific literature regarding prevailing taxonomic concepts and the morphological diversity found in Cecidomyiidae. These causes as well as obvious differences between neontological and paleontological taxonomic practices are discussed. Amediini trib. nov. Jaschhof, 2021 is introduced as a new tribe of the Micromyinae, to absorb the genera Amedia Jaschhof, 1997 (extant, North America, type genus), Amediella Jaschhof, 2003 (extant, New Zealand) and Eltxo Arillo & Nel, 2000 (extinct, Alava amber). A diagnosis of the new tribe is given. Krassiloviolini Fedotova & Perkovsky, 2017 is a new junior synonym of Heteropezini Schiner, 1868. Amediini Plakidas, 2017 and Zarqacecidomyius singularis Kaddumi, 2007 are nomina nuda.

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