scholarly journals Paleobiogeography, paleoecology, diversity, and speciation patterns in the Eublastoidea (Blastozoa: Echinodermata)

Paleobiology ◽  
2020 ◽  
pp. 1-15
Author(s):  
Jennifer E. Bauer
Keyword(s):  
Evolutionary History ◽  
R Package ◽  
Sympatric Speciation ◽  
Probabilistic Methods ◽  
Global Changes ◽  
Environmental Preferences ◽  
Biogeographic Patterns ◽  
Dispersal Events ◽  
Future Work ◽  
Diversity Dynamics

Abstract Understanding the distribution of taxa in space and time is key to understanding diversity dynamics. The fossil record provides an avenue to assess these patterns on vast timescales and through major global changes. The Eublastoidea were a conservatively plated Paleozoic echinoderm clade that range from the middle Silurian to the end-Permian. The geographic distribution of the eublastoids, as a whole, has been qualitatively assessed but has historically lacked a quantitative analysis. This is the first examination of the Eublastoidea using probabilistic methods within the R package BioGeoBEARS to assess macroevolutionary trends. Results provide an updated understanding of eublastoid diversity with new peaks and troughs in diversity through their evolutionary history. Lithology is examined in an evolutionary framework and does not have clear evolutionary trends, and there is much work to be done regarding environmental preferences. Biogeographic patterns do not recover precise group origins but do support the previous work that outlines Eublastoidea as a Laurentian clade. Sympatric speciation events dominant the clade's history but are likely exaggerated due to the highly combined areas. Vicariance events are rare and restricted to the Silurian and Devonian, and dispersal events are more common throughout the evolutionary history. Pathways allowing for lineage migrations are noted between southern Laurussia and China in the Devonian and Carboniferous and southern Laurussia and eastern Gondwana in the Carboniferous. Future work will include the addition of more non-Laurentian species into the estimated phylogeny to better estimate these global patterns.

Most parsimonious areagrams versus fossils: the case of Nothofagus (Nothofagaceae)

2001 ◽  
Vol 49 (3) ◽  
pp. 367 ◽  
Author(s):  
Ulf Swenson ◽  
Robert S. Hill
Keyword(s):  
Software Component ◽  
Historical Biogeography ◽  
Geological Data ◽  
Biogeographic Patterns ◽  
Vicariance Biogeography ◽  
Dispersal Events ◽  
Geological Context

Vicariance biogeography uses most parsimonious areagrams in order to explain biogeographic patterns. One notion is that areagrams convey biogeographic information to the extent that alternative palaeogeographic hypotheses are suggested. However, extinctions may distort biogeographic information, leading to areagrams showing area relationships not supported by geological data, and plausible dispersal events might also be overlooked. By the use of the software COMPONENT 2.0, Nothofagus phylogeny was reconciled with the most parsimonious areagrams. Well-preserved fossils, identified to subgenera, were optimised to the reconciled tree. Not all past distributions were predicted by the analysis, and Nothofagus has clearly been present in areas where it cannot have been if strict vicariance is followed. It can therefore be demonstrated that the biogeographic signal in Nothofagus areagrams is incomplete, and that most parsimonious areagrams can be flawed. Areagrams can be a useful tool in historical biogeography, but must be scrutinised within a known geological context and not accepted uncritically as alternative palaeogeographical hypotheses.

scholarly journals The largest known cowrie and the iterative evolution of giant cypraeid gastropods

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Stefano Dominici ◽  
Mariagabriella Fornasiero ◽  
Luca Giusberti
Keyword(s):  
Species Richness ◽  
Evolutionary History ◽  
Western Europe ◽  
Negative Relationship ◽  
Species Selection ◽  
Biogeographic Patterns ◽  
Large Size ◽  
Northeastern Italy ◽  
History Of ◽  
Iterative Evolution

AbstractBased on the fossil record, we explore the macroevolutionary relationship between species richness and gigantism in cowries (Cypraeidae), the best-studied family of gastropods, with a global diversity distribution that parallels that of tropical corals, mangroves and seagrasses. We introduce Vicetia bizzottoi sp. nov. based on a Priabonian fossil found in northeastern Italy, the largest documented cowrie found so far and the youngest of a lineage of Eocene Gisortiinae species. The Gisortiinae stratigraphic record in western Europe indicates that species selection favoured large size and armouring of the shell. Palaeoecology and per-stage species richness suggest that gigantism occurred in peripheral habitats with respect to diversity hotspots, where smaller species were favoured. The Eocene–Oligocene boundary was marked by a turnover and the Chattian global warming favoured small-sized species of derived clades. Species selection leading to gigantism is further documented in Miocene lineages of Zoila and Umbilia, in the southern hemisphere, two extant genera distributed at the periphery of modern diversity hotspots, suggesting that the negative relationship between size and diversity is a recurring pattern in the evolutionary history of cowries. This palaeontological evidence is projected onto the existing hypotheses that explain analogous biogeographic patterns in various other taxa. Likewise, body size-species richness negative relationship was possibly driven in cowries by physiological, ecological and life history constraints.

The evolutionary history of Lipsothrix Loew (Diptera : Tipuloidea) inferred through systematic revision and historical biogeographical analysis

2015 ◽  
Vol 29 (3) ◽  
pp. 239
Author(s):  
Matthew Petersen
Keyword(s):  
Evolutionary History ◽  
Indian Plate ◽  
Valid Species ◽  
Systematic Revision ◽  
Ancestral Area ◽  
Western Palearctic ◽  
History Of ◽  
Biogeographical Analysis ◽  
Dispersal Events ◽  
One New Species

The evolutionary history of the crane fly genus Lipsothrix Lowe, 1873 was examined through a systematic revision of specimens maintained in natural history collections, parsimony analysis using TNT based on immature and adult morphology, and dispersal–vicariance analyses in RASP (Bayesian and S-DIVA). The genus Lipsothrix was found to contain 29 valid species, one subspecies (L. nobilis iranica) and three species maintained but in need of further evaluation (Lipsothrix burmica, L. heitfeldi, L. yakushimae). One species complex (L. shasta complex) was further resolved using ordination and cluster analyses. One new species is described, L. nullusarma, sp. nov., and three species are synonymised (L. fulva, L. mirifica, L. yamamotoana omogoensis). Phylogenetic analysis recovered a strongly supported and monophyletic Lipsothrix. The historical biogeographical analyses of Lipsothrix inferred an ancestral area in the Western Palearctic region that likely dates to the Eocene. One, or several, dispersal events occurred from the Western Palearctic before major diversification events occurred in the Oriental and Eastern Palearctic + Nearctic regions. Two major paleogeographical developments occurring in the Oriental and Eastern Palearctic + Nearctic regions are largely responsible for Lipsothrix diversification, the collision of the Indian plate with Asia and the rise of the trans-Beringian land bridges during the Tertiary and Quaternary.

scholarly journals Phylogenomics and biogeography of the world's thrushes (Aves, Turdus ): new evidence for a more parsimonious evolutionary history

2020 ◽  
Vol 287 (1919) ◽  
pp. 20192400 ◽  
Author(s):  
Romina Batista ◽  
Urban Olsson ◽  
Tobias Andermann ◽  
Alexandre Aleixo ◽  
Camila Cherem Ribas ◽  
...  
Keyword(s):  
Evolutionary History ◽  
Species Level ◽  
Probabilistic Methods ◽  
Single Event ◽  
Genomic Dataset ◽  
Multispecies Coalescent ◽  
The Rich ◽  
Western Palaearctic ◽  
New Evidence ◽  
African Clade

To elucidate the relationships and spatial range evolution across the world of the bird genus Turdus (Aves), we produced a large genomic dataset comprising ca 2 million nucleotides for ca 100 samples representing 53 species, including over 2000 loci. We estimated time-calibrated maximum-likelihood and multispecies coalescent phylogenies and carried out biogeographic analyses. Our results indicate that there have been considerably fewer trans-oceanic dispersals within the genus Turdus than previously suggested, such that the Palaearctic clade did not originate in America and the African clade was not involved in the colonization of the Americas. Instead, our findings suggest that dispersal from the Western Palaearctic via the Antilles to the Neotropics might have occurred in a single event, giving rise to the rich Neotropical diversity of Turdus observed today, with no reverse dispersals to the Palaearctic or Africa. Our large multilocus dataset, combined with dense species-level sampling and analysed under probabilistic methods, brings important insights into historical biogeography and systematics, even in a scenario of fast and spatially complex diversification.

scholarly journals Counting Connected Hypergraphs via the Probabilistic Method

2016 ◽  
Vol 25 (1) ◽  
pp. 21-75 ◽  
Author(s):  
BÉLA BOLLOBÁS ◽  
OLIVER RIORDAN
Keyword(s):  
Central Limit Theorem ◽  
Limit Theorem ◽  
Local Limit Theorem ◽  
Probabilistic Method ◽  
Local Limit ◽  
Probabilistic Methods ◽  
Uniform Hypergraphs ◽  
Asymptotic Formulae ◽  
Random Hypergraph ◽  
Future Work

In 1990 Bender, Canfield and McKay gave an asymptotic formula for the number of connected graphs on [n] = {1,2,. . .,n} withmedges, whenevernand the nullitym−n+1 tend to infinity. LetCr(n,t) be the number of connectedr-uniform hypergraphs on [n] with nullityt= (r−1)m−n+1, wheremis the number of edges. Forr≥ 3, asymptotic formulae forCr(n,t) are known only for partial ranges of the parameters: in 1997 Karoński and Łuczak gave one fort=o(logn/log logn), and recently Behrisch, Coja-Oghlan and Kang gave one fort=Θ(n). Here we prove such a formula for any fixedr≥ 3 and anyt=t(n) satisfyingt=o(n) andt→∞ asn→∞, complementing the last result. This leaves open only the caset/n→∞, which we expect to be much simpler, and will consider in future work. The proof is based on probabilistic methods, and in particular on a bivariate local limit theorem for the number of vertices and edges in the largest component of a certain random hypergraph. We deduce this from the corresponding central limit theorem by smoothing techniques.

The unity, diversity and conformity of bugs (Hemiptera) through time

2016 ◽  
Vol 107 (2-3) ◽  
pp. 109-128 ◽  
Author(s):  
Jacek Szwedo
Keyword(s):  
Fossil Record ◽  
Evolutionary History ◽  
Biotic Interactions ◽  
Global Changes ◽  
Short History ◽  
Insect Order ◽  
History Of ◽  
Big Four

ABSTRACTThis paper outlines and discusses the fossil record of the Hemiptera – the fifth most diverse insect order. The diversity of these insects in comparison with the “Big Four” group is given, together with a short history of its classification. Updated information is presented about the fossil record of particular families, with a brief analysis. The main evolutionary traits of the major Hemiptera lineages are briefly described. The influence of biotic interactions with endosymbionts, shaping the evolution of the hemipterans as well as abiotic events and major global changes, is disputed. The innovations and perils of the evolutionary history of the Hemiptera are presented.

scholarly journals Estimating Diversity Through Time using Molecular Phylogenies: Old and Species-Poor Frog Families are the Remnants of a Diverse Past

2019 ◽  
Author(s):  
O. Billaud ◽  
D. S. Moen ◽  
T. L. Parsons ◽  
H. Morion
Keyword(s):  
Probabilistic Approach ◽  
R Package ◽  
Phylogenetic Comparative Methods ◽  
Extinction Rate ◽  
Competitive Effects ◽  
Phenotypic Divergence ◽  
Poor Group ◽  
Diversity Dynamics ◽  
Diversity Estimates ◽  
Better Than

Estimating how the number of species in a given group varied in the deep past is of key interest to evolutionary biologists. However, current phylogenetic approaches for obtaining such estimates have limitations, such as providing unrealistic diversity estimates at the origin of the group. Here we develop a robust probabilistic approach for estimating Diversity-Through-Time (DTT) curves and uncertainty around these estimates from phylogenetic data. We show with simulations that under various realistic scenarios of diversification, this approach performs better than previously proposed approaches. We also characterize the effect of tree size and undersampling on the performance of the approach. We apply our method to understand patterns of species diversity in anurans (frogs and toads). We find that Archaeobatrachia – a species-poor group of old frog clades often found in temperate regions – formerly had much higher diversity and net diversification rate, but the group declined in diversity as younger, nested clades diversified. This diversity decline seems to be linked to a decline in speciation rate rather than an increase in extinction rate. Our approach, implemented in the R package RPANDA, should be useful for evolutionary biologists interested in understanding how past diversity dynamics have shaped present-day diversity. It could also be useful in other contexts, such as for analyzing clade-clade competitive effects or the effect of species richness on phenotypic divergence. [phylogenetic comparative methods; birth-death models; diversity curves; diversification; extinction; anurans]

scholarly journals A simple tool for linking photo-identification with multimedia data to track mammal behaviour

2021 ◽  
Author(s):  
Alexandre M. S. Machado ◽  
Mauricio Cantor
Keyword(s):  
Bottlenose Dolphins ◽  
R Package ◽  
Multimedia Data ◽  
Raw Material ◽  
Individual Identification ◽  
Photo Identification ◽  
In The Wild ◽  
The Individual ◽  
Future Work ◽  
Free Ranging

AbstractIdentifying individual animals is critical to describe demographic and behavioural patterns, and to investigate the ecological and evolutionary underpinnings of these patterns. The traditional non-invasive method of individual identification in mammals—comparison of photographed natural marks—has been improved by coupling other sampling methods, such as recording overhead video, audio and other multimedia data. However, aligning, linking and syncing these multimedia data streams are persistent challenges. Here, we provide computational tools to streamline the integration of multiple techniques to identify individual free-ranging mammals when tracking their behaviour in the wild. We developed an open-source R package for organizing multimedia data and for simplifying their processing a posteriori—“MAMMals: Managing Animal MultiMedia: Align, Link, Sync”. The package contains functions to (i) align and link the individual data from photographs to videos, audio recordings and other text data sources (e.g. GPS locations) from which metadata can be accessed; and (ii) synchronize and extract the useful multimedia (e.g. videos with audios) containing photo-identified individuals. To illustrate how these tools can facilitate linking photo-identification and video behavioural sampling in situ, we simultaneously collected photos and videos of bottlenose dolphins using off-the-shelf cameras and drones, then merged these data to track the foraging behaviour of individuals and groups. We hope our simple tools encourage future work that extend and generalize the links between multiple sampling platforms of free-ranging mammals, thereby improving the raw material needed for generating new insights in mammalian population and behavioural ecology.

scholarly journals When to use Quantile Normalization?

2014 ◽  
Author(s):  
Stephanie C. Hicks ◽  
Rafael A. Irizarry
Keyword(s):  
R Package ◽  
Current Approach ◽  
Global Changes ◽  
Quantile Normalization ◽  
Subject Matter Experts ◽  
Monte Carlo Simulation Study ◽  
Multiple Gene ◽  
Normalization Methods ◽  
The Subject ◽  
Generation Sequencing

Normalization and preprocessing are essential steps for the analysis of high-throughput data including next-generation sequencing and microarrays. Multi-sample global normalization methods, such as quantile normalization, have been successfully used to remove technical variation from noisy data. These methods rely on the assumption that observed global changes across samples are due to unwanted technical variability. Transforming the data to remove these differences has the potential to remove interesting biologically driven global variation and therefore may not be appropriate depending on the type and source of variation. Currently, it is up to the subject matter experts, for example biologists, to determine if the stated assumptions are appropriate or not. Here, we propose a data-driven method to test for the assumptions of global normalization methods. We demonstrate the utility of our method (quantro), by applying it to multiple gene expression and DNA methylation and show examples of when global normalization methods are not appropriate. We also perform a Monte Carlo simulation study to illustrate how our method generally outperforms the current approach. An R-package implementing our method is available on Bioconductor (http://www.bioconductor.org/packages/release/bioc/html/quantro.html).

Phylogeny and Biogeography of Acaena (Rosaceae) and its Relatives: Evidence of Multiple Long-Distance Dispersal Events Across the Globe

2021 ◽  
Vol 46 (4) ◽  
pp. 998-1010
Author(s):  
Javier Jauregui-Lazo ◽  
Daniel Potter
Keyword(s):  
South Africa ◽  
New Zealand ◽  
Southern Hemisphere ◽  
Phylogenetic Analyses ◽  
Strong Support ◽  
Disjunct Distribution ◽  
Long Distance Dispersal ◽  
Long Distance ◽  
Biogeographic Patterns ◽  
Dispersal Events

Abstract— Acaena (Rosaceae) is the most complex and ecologically variable genus in Sanguisorbinae. Although it has been the subject of several taxonomic treatments, the largest phylogenetic analysis to date only sampled a small fraction of the total global diversity (five to seven out of 45 to 50 species). This study included most of the species to elucidate the phylogenetic relationships of Acaena and biogeographic patterns in Sanguisorbinae. Phylogenetic analyses of non-coding nuclear (ITS region) and chloroplast (trnL-F) DNA sequence markers using maximum likelihood and Bayesian analyses suggested that Acaena is a paraphyletic group with species of Margyricarpus and Tetraglochin nested within it. We identified strong support for eight subclades that are geographically or taxonomically structured. Nevertheless, the species-level relationships within subclades are still uncertain, which may be due to rapid diversification and lack of informative characters in the markers used. Sanguisorbinae, a primarily Southern Hemisphere clade, exhibits a classic Gondwana disjunct distribution. This current distribution is explained primarily by eight long-distance dispersal events. Our results suggested that Sanguisorbinae split into Cliffortia and Acaena around 13.6 mya. While Cliffortia diversified in southern South Africa, Acaena experienced several migration events in the Southern Hemisphere. Our estimation of the ancestral range suggested that Acaena likely originated in South Africa, followed by migration and subsequent diversification into southern South America. From there, the genus migrated to New Zealand, throughout the Andes, and to tropical areas in Central America, reaching as far north as California. Chile and New Zealand are the main sources of propagules for dispersal as well as the greatest diversity for the genus. The evolutionary relationships of species in Acaena combine a history of rapid diversifications, long-distance dispersals, and genetic variation within some taxa. Further research should be undertaken to clarify the infraspecific classification of A. magellanica.

Sign in / Sign up

Export Citation Format

Share Document