Avian Diversity: Speciation, Macroevolution, and Ecological Function

2020 ◽  
Vol 51 (1) ◽  
pp. 533-560 ◽  
Author(s):  
Joseph A. Tobias ◽  
Jente Ottenburghs ◽  
Alex L. Pigot
Keyword(s):  
Evolutionary Biology ◽  
Biological Diversity ◽  
Functional Trait ◽  
Functional Ecology ◽  
Bird Diversity ◽  
Data Sets ◽  
Evolutionary Origins ◽  
Integrative Studies ◽  
And Function ◽  
Biology Research

The origin, distribution, and function of biological diversity are fundamental themes of ecology and evolutionary biology. Research on birds has played a major role in the history and development of these ideas, yet progress was for many decades limited by a focus on patterns of current diversity, often restricted to particular clades or regions. Deeper insight is now emerging from a recent wave of integrative studies combining comprehensive phylogenetic, environmental, and functional trait data at unprecedented scales. We review these empirical advances and describe how they are reshaping our understanding of global patterns of bird diversity and the processes by which it arises, with implications for avian biogeography and functional ecology. Further expansion and integration of data sets may help to resolve longstanding debates about the evolutionary origins of biodiversity and offer a framework for understanding and predicting the response of ecosystems to environmental change.

scholarly journals Further twists in gastropod shell evolution

2008 ◽  
Vol 4 (2) ◽  
pp. 179-182 ◽  
Author(s):  
Reuben Clements ◽  
Thor-Seng Liew ◽  
Jaap Jan Vermeulen ◽  
Menno Schilthuizen
Keyword(s):  
Evolutionary Biology ◽  
Logarithmic Spiral ◽  
Spiral Growth ◽  
Evolutionary Perspective ◽  
Gastropod Shell ◽  
Form And Function ◽  
Evolutionary Origins ◽  
Taxonomic Groups ◽  
And Function ◽  
Shell Coiling

The manner in which a gastropod shell coils has long intrigued laypersons and scientists alike. In evolutionary biology, gastropod shells are among the best-studied palaeontological and neontological objects. A gastropod shell generally exhibits logarithmic spiral growth, right-handedness and coils tightly around a single axis. Atypical shell-coiling patterns (e.g. sinistroid growth, uncoiled whorls and multiple coiling axes), however, continue to be uncovered in nature. Here, we report another coiling strategy that is not only puzzling from an evolutionary perspective, but also hitherto unknown among shelled gastropods. The terrestrial gastropod Opisthostoma vermiculum sp. nov. generates a shell with: (i) four discernable coiling axes, (ii) body whorls that thrice detach and twice reattach to preceding whorls without any reference support, and (iii) detached whorls that coil around three secondary axes in addition to their primary teleoconch axis. As the coiling strategies of individuals were found to be generally consistent throughout, this species appears to possess an unorthodox but rigorously defined set of developmental instructions. Although the evolutionary origins of O. vermiculum and its shell's functional significance can be elucidated only once fossil intermediates and live individuals are found, its bewildering morphology suggests that we still lack an understanding of relationships between form and function in certain taxonomic groups.

General models of ecological diversification. II. Simulations and empirical applications

Paleobiology ◽  
2016 ◽  
Vol 42 (2) ◽  
pp. 209-239 ◽  
Author(s):  
Philip M. Novack-Gottshall
Keyword(s):  
Classification Tree ◽  
Functional Trait ◽  
Functional Ecology ◽  
Data Sets ◽  
Ecological Diversification ◽  
Weighting Potential ◽  
General Dynamics ◽  
Life Habits ◽  
Redundancy Models ◽  
Best Fit

AbstractModels of functional ecospace diversification within life-habit frameworks (functional-trait spaces) are increasingly used across community ecology, functional ecology, and paleoecology. In general, these models can be represented by four basic processes, three that have driven causes and one that occurs through a passive process. The driven models include redundancy (caused by forms of functional canalization), partitioning (specialization), and expansion (divergent novelty), but they also share important dynamical similarities with the passive neutral model. In this second of two companion articles, Monte Carlo simulations of these models are used to illustrate their basic statistical dynamics across a range of data structures and implementations. Ecospace frameworks with greater numbers of characters (functional traits) and ordered (multistate) character types provide more distinct dynamics and greater ability to distinguish the models, but the general dynamics tend to be congruent across all implementations. Classification-tree methods are proposed as a powerful means to select among multiple candidate models when using multivariate data sets. Well-preserved Late Ordovician (type Cincinnatian) samples from the Kope and Waynesville formations are used to illustrate how these models can be inferred in empirical applications. Initial simulations overestimate the ecological disparity of actual assemblages, confirming that actual life habits are highly constrained. Modifications incorporating more realistic assumptions (such as weighting potential life habits according to actual frequencies and adding a parameter controlling the strength of each model’s rules) provide better correspondence to actual assemblages. Samples from both formations are best fit by partitioning (and to lesser extent redundancy) models, consistent with a role for local processes. When aggregated as an entire formation, the Kope Formation pool remains best fit by the partitioning model, whereas the entire Waynesville pool is better fit by the redundancy model, implying greater beta diversity within this unit. The ‘ecospace’ package is provided to implement the simulations and to calculate their dynamics using the R statistical language.

scholarly journals Understanding microbiomes through trait-based ecology

2018 ◽  
Vol 39 (1) ◽  
pp. 53
Author(s):  
Jennifer L Wood ◽  
Ashley E Franks
Keyword(s):  
Functional Traits ◽  
Ecosystem Health ◽  
Antibiotic Production ◽  
Functional Trait ◽  
Functional Ecology ◽  
Ecological Framework ◽  
Major Goal ◽  
Physiological Trait ◽  
Regeneration Time ◽  
And Function

Ecology is the study of the interactions amongst organisms and their environment1. In microbial ecology, a major goal is to understand how environmental microbiomes impact ecosystem health and function. This desire to mechanistically link micro and macro processes is increasingly highlighting the importance of functional ecology, which aims to develop an understanding of relationships using functional traits, as opposed to species names. A functional trait may be any morphological or physiological trait that influences the performance or fitness of an individual in a given environment, such as regeneration time, size, antibiotic production or motility2. Although it is not possible to measure a given trait for each individual within an environmental microbiome, community-level functional traits can be derived from the community metagenome either directly via shotgun sequencing or predictively (for bacteria) from 16S rRNA profiles3. In understanding environmental microbiomes, functional traits have unique properties that can be utilised to (1) compare microbiomes using an ecological framework, (2) understand processes governing community assembly, and (3) build predictive ecological models.

Homology, Genes, and Evolutionary Innovation

2014 ◽  
Author(s):  
Günter P. Wagner
Keyword(s):  
Evolutionary Biology ◽  
Regulatory Networks ◽  
Biological Diversity ◽  
Cell Types ◽  
Origin And Evolution ◽  
Major Transitions ◽  
Form And Function ◽  
Historical Continuity ◽  
Evolutionary Innovation ◽  
Character Identity

Homology—a similar trait shared by different species and derived from common ancestry, such as a seal's fin and a bird's wing—is one of the most fundamental yet challenging concepts in evolutionary biology. This book provides the first mechanistically based theory of what homology is and how it arises in evolution. The book argues that homology, or character identity, can be explained through the historical continuity of character identity networks—that is, the gene regulatory networks that enable differential gene expression. It shows how character identity is independent of the form and function of the character itself because the same network can activate different effector genes and thus control the development of different shapes, sizes, and qualities of the character. Demonstrating how this theoretical model can provide a foundation for understanding the evolutionary origin of novel characters, the book applies it to the origin and evolution of specific systems, such as cell types; skin, hair, and feathers; limbs and digits; and flowers. The first major synthesis of homology to be published in decades, this book reveals how a mechanistically based theory can serve as a unifying concept for any branch of science concerned with the structure and development of organisms, and how it can help explain major transitions in evolution and broad patterns of biological diversity.

The Evolutionary Biology of Species

2019 ◽  
Author(s):  
Timothy G. Barraclough
Keyword(s):  
Evolutionary Biology ◽  
Biological Diversity ◽  
Distinct Species ◽  
Species Boundaries ◽  
Central Thesis ◽  
Species Accumulation ◽  
Multicellular Organisms ◽  
Broad Approach ◽  
Over Time

‘Species’ are central to understanding the origin and dynamics of biological diversity; explaining why lineages split into multiple distinct species is one of the main goals of evolutionary biology. However, the existence of species is often taken for granted, and precisely what is meant by species and whether they really exist as a pattern of nature has rarely been modelled or critically tested. This novel book presents a synthetic overview of the evolutionary biology of species, describing what species are, how they form, the consequences of species boundaries and diversity for evolution, and patterns of species accumulation over time. The central thesis is that species represent more than just a unit of taxonomy; they are a model of how diversity is structured as well as how groups of related organisms evolve. The author adopts an intentionally broad approach to consider what species constitute, both theoretically and empirically, and how we detect them, drawing on a wealth of examples from microbes to multicellular organisms.

The New Statistics with R

2021 ◽  
Author(s):  
Andy Hector
Keyword(s):  
Linear Model ◽  
Evolutionary Biology ◽  
Environmental Science ◽  
Research Training ◽  
Model Analysis ◽  
Scientific Data ◽  
Information Criteria ◽  
Reproducible Research ◽  
Data Sets ◽  
R Programming

Statistics is a fundamental component of the scientific toolbox, but learning the basics of this area of mathematics is one of the most challenging parts of a research training. This book gives an up-to-date introduction to the classical techniques and modern extensions of linear-model analysis—one of the most useful approaches in the analysis of scientific data in the life and environmental sciences. The book emphasizes an estimation-based approach that takes account of recent criticisms of overuse of probability values and introduces the alternative approach using information criteria. The book is based on the use of the open-source R programming language for statistics and graphics, which is rapidly becoming the lingua franca in many areas of science. This second edition adds new chapters, including one discussing some of the complexities of linear-model analysis and another introducing reproducible research documents using the R Markdown package. Statistics is introduced through worked analyses performed in R using interesting data sets from ecology, evolutionary biology, and environmental science. The data sets and R scripts are available as supporting material.

scholarly journals SLC26A2 gene expression levels in melanoma

2021 ◽  
Vol 31 (Supplement_2) ◽  
Author(s):  
Diana Assis ◽  
Ana Luísa De Sousa-Coelho
Keyword(s):  
Gene Expression ◽  
Cancer Cells ◽  
Normal Skin ◽  
Braf Inhibitor ◽  
Ovarian Cancer Cells ◽  
Data Sets ◽  
Dependent Manner ◽  
Therapeutic Decisions ◽  
Pharmacological Screening ◽  
And Function

Abstract Background A recent repurposing pharmacological screening revealed that vanadium-containing drugs anti-proliferative action in ovarian cancer cells was SLC26A2-dependent. SLC26A2/DTDST is a sulfate transporter, related to chondrodysplasia syndromes. Despite some reports on colon cancer, there are no studies on SLC26A2 performed in melanoma in the literature. Methods To better understand its potential use as biomarker for therapeutic decisions in melanoma, we performed gene expression analyses of the data available at GEO profiles (NCBI). Gene data sets that allowed analysis of SLC26A2 expression (1) in melanoma; (2) in response to drugs; (3) regulated by other proteins, were selected. Results Our results showed that, compared to normal skin or benign nevi, SLC26A2 expression was 2.5-fold higher in malignant melanoma (P = 0.019). Compared to the primary tumor, SLC26A2 expression tripled in melanoma (P = 0.022). We found a 6% decrease of SLC26A2 expression in A375 melanoma cells treated with BRAF inhibitor Vemurafenib (P < 0.001). After treatment of A375 cells with MLN4924, a selective inhibitor of the activating enzyme of Nedd8, SLC26A2 decreased in a time-dependent manner ( > 80% at 24 h; P < 0.001). In Sk-Mel-2 cells overexpressing E2F-1, a transcription factor that induces apoptosis in cancer cells, SLC26A2 levels were reduced by 76.4% (P = 0.067). In A375P cells depleted of PGC1α, an important metabolic co-activator in mitochondrial biogenesis and function, SLC26A2 levels increased 16% (P = 0.013). Conclusions From this work, we unveiled, for the first time, potential clues to better understand the regulation and role of SLC26A2 in melanoma. Though, it is still to be determined whether SLC26A2 is a driver or a passenger in the disease.

scholarly journals Interactions Between the Invasive New Zealand Mudsnail (Potamopyrgus Antipodarum) and a Native Snail (Fossaria Bakerilymnaea Bulimoides Group) in the Greater Yeelowstone

2011 ◽  
Vol 33 ◽  
pp. 161-170
Author(s):  
Heather Thon ◽  
Amy Krist
Keyword(s):  
Invasive Species ◽  
New Zealand ◽  
American West ◽  
Biological Diversity ◽  
Potamopyrgus Antipodarum ◽  
The Past ◽  
Conservation Concern ◽  
And Function ◽  
New Zealand Mud Snail ◽  
The Impact

Understanding invasive species impacts is critical to determining how an ecosystem may function after an introduction. Invasive species can alter the structure and function of ecosystems, reduce biological diversity, and alter communities through predation, facilitation and competition. In the past 30 years, the invasive New Zealand mud snail (Potamopyrgus antipodarum) has established in areas of conservation concern in the American West including Yellowstone National Park. To develop a greater understanding of the impact of P. antipodarum on the native co-occurring snail, Fossaria (Bakerilymnaea) bulimoides group, we conducted two experiments to assess the interactions occurring between these snails. We found that F. bulimoides growth was reduced by all interactors, but especially by P. antipodarum. In addition, growth of F. bulimoides was much more affected by high biomass of snails than P. antipodarum. P. antipodarum grew more in the presence of interactors and their growth was facilitated by the presence of the native snail F. bulimoides.

scholarly journals Efficient detection of repeating sites to accelerate phylogenetic likelihood calculations

2016 ◽  
Author(s):  
Kassian Kobert ◽  
Alexandros Stamatakis ◽  
Tomáš Flouri
Keyword(s):  
Evolutionary Biology ◽  
Likelihood Function ◽  
Simulated Data ◽  
Evolutionary Model ◽  
Identical Result ◽  
Model Parameters ◽  
Data Sets ◽  
Efficient Detection ◽  
Novel Method ◽  
Computational Bottleneck

The phylogenetic likelihood function is the major computational bottleneck in several applications of evolutionary biology such as phylogenetic inference, species delimitation, model selection and divergence times estimation. Given the alignment, a tree and the evolutionary model parameters, the likelihood function computes the conditional likelihood vectors for every node of the tree. Vector entries for which all input data are identical result in redundant likelihood operations which, in turn, yield identical conditional values. Such operations can be omitted for improving run-time and, using appropriate data structures, reducing memory usage. We present a fast, novel method for identifying and omitting such redundant operations in phylogenetic likelihood calculations, and assess the performance improvement and memory saving attained by our method. Using empirical and simulated data sets, we show that a prototype implementation of our method yields up to 10-fold speedups and uses up to 78% less memory than one of the fastest and most highly tuned implementations of the phylogenetic likelihood function currently available. Our method is generic and can seamlessly be integrated into any phylogenetic likelihood implementation.

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