scholarly journals Detecting shifts in diversity limits from molecular phylogenies: what can we know?

2011 ◽  
Vol 278 (1722) ◽  
pp. 3294-3302 ◽  
Author(s):  
Lynsey McInnes ◽  
C. David L. Orme ◽  
A. Purvis
Keyword(s):  
Species Diversity ◽  
Species Turnover ◽  
Species Level ◽  
Perfect Phylogeny ◽  
Extinction Rates ◽  
Rapid Speciation ◽  
Extant Species ◽  
History Of ◽  
Molecular Phylogenies ◽  
Fossil Records

Large complete species-level molecular phylogenies can provide the most direct information about the macroevolutionary history of clades having poor fossil records. However, extinction will ultimately erode evidence of pulses of rapid speciation in the deep past. Assessment of how well, and for how long, phylogenies retain the signature of such pulses has hitherto been based on a—probably untenable—model of ongoing diversity-independent diversification. Here, we develop two new tests for changes in diversification ‘rules’ and evaluate their power to detect sudden increases in equilibrium diversity in clades simulated with diversity-dependent speciation and extinction rates. Pulses of diversification are only detected easily if they occurred recently and if the rate of species turnover at equilibrium is low; rates reported for fossil mammals suggest that the power to detect a doubling of species diversity falls to 50 per cent after less than 50 Myr even with a perfect phylogeny of extant species. Extinction does eventually draw a veil over past dynamics, suggesting that some questions are beyond the limits of inference, but sudden clade-wide pulses of speciation can be detected after many millions of years, even when overall diversity is constrained. Applying our methods to existing phylogenies of mammals and angiosperms identifies intervals of elevated diversification in each.

scholarly journals Crustacean biodiversity through the marine fossil record

2000 ◽  
Vol 69 (4) ◽  
pp. 213-222 ◽  
Author(s):  
J. John Sepkoski
Keyword(s):  
Fossil Record ◽  
Major Group ◽  
Mass Extinctions ◽  
Data Bases ◽  
Extinction Rates ◽  
Marine Crustaceans ◽  
History Of ◽  
Fossil Preservation ◽  
Fossil Records ◽  
High Diversity

Approximately 2,600 genera of marine crustaceans have been recognized in the fossil record, and crustaceans constitute the major component of marine arthropod diversity from the mid- Paleozoic to the Recent. Despite problems of sporadic fossil preservation and/or taxonomic ambiguity, some general statements can be made about the history of crustacean biodiversity, based on global taxonomic data bases. Ostracodes were the first major group to radiate, attaining high diversity during the Ordovician Period with other members of the Paleozoic evolutionary fauna; rates of extinction and responses to mass extinctions were also similar to those of groups within the Paleozoic fauna. Malacostracans and barnacles (cirripedes), the two other crustacean groups with important fossil records, had minor diversity throughout the Paleozoic Era. Both groups experienced diversification from the mid-Mesozoic to Recent with lower extinction rates, as characteristic members of the Modern evolutionary fauna.

The importance of phylogenetic analysis for the assessment of species turnover: a case history of Paleocene mammals in North America

Paleobiology ◽  
1993 ◽  
Vol 19 (1) ◽  
pp. 1-27 ◽  
Author(s):  
J. David Archibald
Keyword(s):  
North America ◽  
Species Turnover ◽  
Cladistic Analysis ◽  
Species Level ◽  
Mass Extinctions ◽  
Faunal Turnover ◽  
Early Tertiary ◽  
Early Paleocene ◽  
History Of ◽  
Cladistic Analyses

During the latest Cretaceous and the Paleocene in western North America, disappearance rates for mammalian genera track appearance rates, both reaching their peak in the early Paleocene (Puercan) following the extinction of non-avian dinosaurs. Some of the disappearances during this time were pseudoextinctions that resulted when ancestral species disappeared during speciation.Species-level cladistic analyses and a well-constrained biostratigraphic framework are required to study this form of pseudoextinction. Cladistic analyses show that monophyly cannot be established or rejected for some species because these species lack autapomorphies (uniquely derived character states) that unite their constituent members. Such taxa, termed metaspecies, are potential ancestors to species and higher clades with which they share a node in the cladogram.A hypothetical species-level cladistic analysis coupled with three different hypothetical biostratigraphies shows how different models of speciation (bifurcation, budding, or anagenesis) result in very different patterns of true versus pseudoextinction. Depending on the speciation model, true extinction can be overestimated by as much as a factor of four, raising the specter of mass extinction. Species-level studies for three early Tertiary mammalian taxa—taeniodont eutherians, taeniolabidid multituberculates, and periptychid ungulates—use the same procedures. They show that almost 25% of disappearances during the early Paleocene (Puercan) for species in the analysis were pseudoextinctions of metaspecies. Budding and anagenetic-like peripatric speciation, but not bifurcation, are seen in the three examples.Equating disappearance to true extinction can profoundly affect interpretations of faunal turnover, especially during mass extinctions or major faunal reorganizations. Some authors use pseudoextinction to describe the taxonomic rather than evolutionary disappearance of nonmonophyletic groups. Pseudoextinction, as used here refers only to the evolutionary disappearance of metaspecies via speciation. Both usages seem appropriate but should not be confounded.

scholarly journals A Total-Group Phylogenetic Metatree for Cetacea and the Importance of Fossil Data in Diversification Analyses

2021 ◽  
Author(s):  
Graeme T Lloyd ◽  
Graham J Slater
Keyword(s):  
Phylogenetic Trees ◽  
Species Level ◽  
Total Group ◽  
Phylogenetic Studies ◽  
Large Numbers ◽  
Extant Species ◽  
Molecular Phylogenies ◽  
Phylogenetic Hypotheses ◽  
Fossil Data ◽  
Rapid Radiations

Abstract Phylogenetic trees provide a powerful framework for testing macroevolutionary hypotheses, but it is becoming increasingly apparent that inferences derived from extant species alone can be highly misleading. Trees incorporating living and extinct taxa are are needed to address fundamental questions about the origins of diversity and disparity but it has proved challenging to generate robust, species-rich phylogenies that include large numbers of fossil taxa. As a result, most studies of diversification dynamics continue to rely on molecular phylogenies. Here, we extend and apply a recently developed meta-analytic approach for synthesizing previously published phylogenetic studies to infer a well-resolved set of species level, time-scaled phylogenetic hypotheses for extinct and extant cetaceans (whales, dolphins and allies). Our trees extend sampling from the ∼ 90 extant species to over 500 living and extinct species, and therefore allow for more robust inference of macroevolutionary dynamics. While the diversification scenarios we recover are broadly concordant with those inferred from molecular phylogenies they differ in critical ways, notably in the relative contributions of extinction and speciation rate shifts in driving rapid radiations. The metatree approach provides the most immediate route for generating higher level phylogenies of extinct taxa, and opens the door to re-evaluation of macroevolutionary hypotheses derived only from extant taxa.

Recognizing the species of Thuja (Cupressaceae) based on their cone and foliage morphology

Phytotaxa ◽  
2015 ◽  
Vol 219 (2) ◽  
pp. 101 ◽  
Author(s):  
Bin Sun ◽  
Yi-Ming Cui ◽  
Hai-Feng Wang ◽  
David Kay Ferguson ◽  
Qiao-Ping Xiang ◽  
...  
Keyword(s):  
North America ◽  
East Asia ◽  
Evolutionary History ◽  
Morphological Characters ◽  
Species Level ◽  
Fossil Species ◽  
Extant Species ◽  
History Of

Thuja, with 5 extant species, exhibiting a disjunctive distribution between East Asia (3 species) and North America (2 species), was investigated with respect to the morphological characters of foliage and cones by LM and SEM. Here we provide 2 keys to all 5 species of Thuja based on the cones and foliage respectively, which not  only can be used for identifying extant Thuja at the species level, but also have a great potential for recognizing and/or linking the fossil species to living ones, and further tracing the evolutionary history of the genus.

Scydmaenus linqibini sp. nov., a new fossil Scydmaenini in mid-Cretaceous amber from northern Myanmar (Coleoptera: Staphylinidae: Scydmaeninae)

2020 ◽  
Vol 3 (1) ◽  
pp. 036-040
Author(s):  
ZIWEI YIN ◽  
DEYAO ZHOU
Keyword(s):  
Evolutionary History ◽  
Evolutionary Stage ◽  
Diverse Group ◽  
Fossil Species ◽  
Burmese Amber ◽  
Morphological Disparity ◽  
Extant Species ◽  
History Of ◽  
Fossil Records

The tribe Scydmaenini is the second most diverse group of the ant-like stone beetle subfamily Scydmaeninae, with more than 730 extant species classified in seven extant genera (Newton, 2019). However, confirmed fossil records important for elucidating the evolutionary history of the tribe are extremely rare, represented by only two species previously reported from mid-Cretaceous Myanmar amber (Yin et al., 2018; Yin & Cai, 2019). Provided in this paper is the description of a third fossil species of Scydmaenini, again from Burmese amber, which sheds new light on the palaeodiversity and morphological disparity of this group during its early evolutionary stage.

scholarly journals Extinction rates of non-avian dinosaur species are uncorrelated with the rate of evolution of phylogenetically informative characters

2020 ◽  
Vol 16 (6) ◽  
pp. 20200231 ◽  
Author(s):  
Nicholas M. A. Crouch
Keyword(s):  
Species Diversity ◽  
Temporal Variation ◽  
Environmental Conditions ◽  
Morphological Evolution ◽  
Phylogenetic Signal ◽  
Species Level ◽  
Common Mechanism ◽  
Phenotypic Evolution ◽  
Extinction Rates ◽  
Prior Expectation

Determining the factors that shape temporal variation in species diversity is an ongoing challenge. One theory is that species exhibiting lower rates of phenotypic evolution should be more likely to go extinct as they are more susceptible to changing environmental conditions. However, little work has been done to assess whether this process shapes comparatively few lineages, or is a common mechanism shaping changes in species diversity. Here, I analyse the correlation between rates of morphological evolution and extinction at the species level using six published morphological matrices of non-avian dinosaurs. I find no correlation between the two rates at different taxonomic scales, suggesting that extinction in these groups is better described by other factors. As there is a strong prior expectation of correlated rates, I suggest that traditional morphological matrices are inappropriate for addressing this question and that the characters governing lineage persistence are independent of those with high phylogenetic signal. This may be comprehensively determined with continued development of phenomic matrices.

scholarly journals Mesoamerica is a cradle and the Atlantic Forest is a museum of Neotropical butterfly diversity: insights from the evolution and biogeography of Brassolini (Lepidoptera: Nymphalidae)

2021 ◽  
Author(s):  
Pável Matos-Maraví ◽  
Niklas Wahlberg ◽  
André V L Freitas ◽  
Phil Devries ◽  
Alexandre Antonelli ◽  
...  
Keyword(s):  
Species Diversity ◽  
Environmental History ◽  
Atlantic Forest ◽  
Morphological Characters ◽  
Butterfly Species ◽  
Multispecies Coalescent ◽  
Extant Species ◽  
Speciation Rates ◽  
History Of ◽  
Stochastic Mapping

Abstract Regional species diversity is explained ultimately by speciation, extinction and dispersal. Here, we estimate dispersal and speciation rates of Neotropical butterflies to propose an explanation for the distribution and diversity of extant species. We focused on the tribe Brassolini (owl butterflies and allies), a Neotropical group that comprises 17 genera and 108 species, most of them endemic to rainforest biomes. We inferred a robust species tree using the multispecies coalescent framework and a dataset including molecular and morphological characters. This formed the basis for three changes in Brassolini classification: (1) Naropina syn. nov. is subsumed within Brassolina; (2) Aponarope syn. nov. is subsumed within Narope; and (3) Selenophanes orgetorix comb. nov. is reassigned from Catoblepia to Selenophanes. By applying biogeographical stochastic mapping, we found contrasting species diversification and dispersal dynamics across rainforest biomes, which might be explained, in part, by the geological and environmental history of each bioregion. Our results revealed a mosaic of biome-specific evolutionary histories within the Neotropics, where butterfly species have diversified rapidly (cradles: Mesoamerica), have accumulated gradually (museums: Atlantic Forest) or have diversified and accumulated alternately (Amazonia). Our study contributes evidence from a major butterfly lineage that the Neotropics are a museum and a cradle of species diversity.

A history of diversification, extinction, and invasion in tropical America as derived from species-level phylogenies of chionine genera (Family Veneridae)

2001 ◽  
Vol 75 (3) ◽  
pp. 644-657 ◽  
Author(s):  
Peter D. Roopnarine
Keyword(s):  
Species Level ◽  
Eastern Pacific ◽  
Tropical Eastern Pacific ◽  
Western Atlantic ◽  
Early Oligocene ◽  
Tropical America ◽  
History Of ◽  
Extinction Events ◽  
Fossil Records

Phylogenetic reconstructions of two tropical American venerid genera, Chione and Chionopsis (subfamily Chioninae) were attempted at the species-level. The purposes of the analyses were to provide historical reconstructions of origination and extinction events in the two clades, as well as patterns of invasion and diversification. The analyses were based entirely on conchological characters to facilitate the inclusion of a substantial number of fossil taxa, but difficulties were encountered due to the quality of preservation and availability of material. Nevertheless the two genera were established as monophyletic clades, and the reconstructions yielded considerable insight into their histories in tropical America. The analyses suggest that both genera originated in the tropical western Atlantic, Chionopsis by at least the early Oligocene, and Chione in the early Miocene. Various branches of both genera subsequently invaded the tropical eastern Pacific several times prior to Seaway closure, with only one possible reciprocal invasion of the western Atlantic. Pliocene extinction affected both genera more significantly in the western Atlantic relative to the eastern Pacific, and diversity is higher today in the latter region. These conclusions are not entirely consistent with the fossil records of the genera, but this incongruency highlights the need for much more extensive sampling of the eastern Pacific Cenozoic record.

scholarly journals A Total-Group Phylogenetic Metatree for Cetacea and the Importance of Fossil Data in Diversification Analyses

2020 ◽  
Author(s):  
Graeme T. Lloyd ◽  
Graham J. Slater
Keyword(s):  
Phylogenetic Trees ◽  
Species Level ◽  
The Past ◽  
Phylogenetic Studies ◽  
Large Numbers ◽  
Extant Species ◽  
Molecular Phylogenies ◽  
Phylogenetic Hypotheses ◽  
Fossil Data ◽  
Rapid Radiations

AbstractPhylogenetic trees provide a powerful framework for testing macroevolutionary hypotheses, but it is becoming increasingly apparent that inferences derived from extant species alone can be highly misleading. Trees incorporating living and extinct taxa are are needed to address fundamental questions about the origins of diversity and disparity but it has proved challenging to generate robust, species–rich phylogenies that include large numbers of fossil taxa. As a result, most studies of diversification dynamics continue to rely on molecular phylogenies. Here, we extend and apply a recently developed meta–analytic approach for synthesizing previously published phylogenetic studies to infer a well–resolved set of species level, time–scaled phylogenetic hypotheses for extinct and extant cetaceans (whales, dolphins and allies). Our trees extend sampling from the ∼ 90 extant species to over 400 living and extinct species, and therefore allow for more robust inference of macroevolutionary dynamics. While the diversification scenarios we recover are broadly concordant with those inferred from molecular phylogenies they differ in critical ways, most notably in the relative contributions of extinction and speciation rate shifts in driving rapid radiations. Supertrees are often viewed as poor substitute for phylogenies inferred directly from character data but the metatree pipeline overcomes many of the past criticisms leveled at these approaches. Meta–analytic phylogenies provide the most immediate route for integrating fossils into macroevolutionary analyses, the results of which range from untrustworthy to nonsensical without them.

scholarly journals Revealing the factors that promote speciation

1998 ◽  
Vol 353 (1366) ◽  
pp. 241-249 ◽  
Author(s):  
Timothy G. Barraclough ◽  
Alfried P. Vogler ◽  
Paul H. Harvey
Keyword(s):  
Sexual Selection ◽  
Species Diversity ◽  
Time Scale ◽  
Species Level ◽  
Diversity Patterns ◽  
New Methods ◽  
Higher Taxa ◽  
Wide Range ◽  
History Of ◽  
Biological Attributes

What biological attributes of organisms promote speciation, and ultimately, species diversity? This question has a long history of interest, with proposed diversity promoters including attributes such as sexual selection, ecological specialism and dispersability. However, such ideas are difficult to test because the time–scale of processes involved is too great for direct human observation and experimentation. An increasingly powerful solution is to investigate diversity patterns among extant groups to infer the nature of processes operating during the evolution of those groups. This approach relies on the use of robust, phylogenetically based null models to overcome some of the problems inherent in observational inference. We illustrate this area by (i) discussing recent advances in identifying correlates of diversity among higher taxa, and (ii) proposing new methods for analysing patterns in species–level phylogenies, drawing examples from a wide range of organisms.

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