1,721,126 research outputs found
paleoPhylo: free software to draw paleobiological phylogenies
No full textPaleobiological phylogenies often contain contrasting biological information to phylogenies based on extant species. Available software is primarily based on a present-day view of the world, however. Here, we present freeware to visualize phylogenies that is more suitable for the needs of paleobiologists, providing flexibility in how stratigraphic uncertainty, the geological timescale, and ancestor-descendant relationships are depicted
Environmental changes define ecological limits to species richness and reveal the mode of macroevolutionary competition
Full text linkCo-dependent geological and climatic changes obscure how species interact in deep time. The interplay between these environmental factors makes it hard to discern whether ecological competition exerts an upper limit on species richness. Here, using the exceptional fossil record of Cenozoic Era macroperforate planktonic foraminifera, we assess the evidence for alternative modes of macroevolutionary competition. Our models support an environmentally dependent macroevolutionary form of contest competition that yields finite upper bounds on species richness. Models of biotic competition assuming unchanging environmental conditions were overwhelmingly rejected. In the best-supported model, temperature affects the per-lineage diversification rate, while both temperature and an environmental driver of sediment accumulation defines the upper limit. The support for contest competition implies that incumbency constrains species richness by restricting niche availability, and that the number of macroevolutionary niches varies as a function of environmental changes
Inclusion of a near-complete fossil record reveals speciation-related molecular evolution
No full textThe rate of genetic evolution is often too variable among lineages to be explained by a strict molecular clock, prompting alternative ecological and evolutionary hypotheses to explain this rate heterogeneity. One controversial hypothesis is that speciation provokes a burst of rapid genetic change, giving molecular evolution a punctuational component. The amount of root-to-tip genetic change therefore tends to increase with the number of identified speciation events (nodes) along the root-to-tip path in molecular phylogenies. The controversy arises because nodes on molecular phylogenies can typically only be counted if both descendants are extant. Here, using stratigraphic, phylogenetic and ecological data from the exceptional fossil record of Cenozoic macroperforate planktonic foraminifera, we test whether among-lineage rate heterogeneity is explained by ecological factors (abundance, life history and environment) and by the numbers of speciation events according to fossil lineage, fossil morphospecies and molecular species concepts. The number of nodes between root and tips on the fossil lineage phylogeny was a statistically significant correlate of the rate of molecular evolution over the same root-to-tip path. The speciation counts from other species concepts and hypothesized ecological drivers had considerably less support. Our results showcase how the fossil record contains signals of biological processes that drive genetic evolution, justifying calls to further marry fossil and molecular data when studying macroevolution over geological time-scales
Algorithmic approaches to aid species' delimitation in multidimensional morphospace
Full text linkBackgroundThe species is a fundamental unit of biological pattern and process, but its delimitation has proven a ready source of argument and disagreement. Here, we discuss four key steps that utilize statistical thresholds to describe the morphological variability within a sample and hence assess whether there is evidence for one or multiple species. Once the initial set of biologically relevant traits on comparable individuals has been identified, there is no need for the investigator to hypothesise how specimens might be divided among groups, nor the traits on which groups might be separated. ResultsPrincipal components are obtained using robust covariance estimates and retained only if they exceed threshold amounts of explanatory power, before model-based clustering is performed on the dimension-reduced space. We apply these steps in an attempt to resolve ongoing debates among taxonomists working on the extinct Eocene planktonic foraminifera Turborotalia, providing statistical evidence for two species shortly before the lineage's extinction near the Eocene/Oligocene boundary. ConclusionBy estimating variance robustly (samples containing incipient species are unlikely to be scaled optimally by means and standard deviations) and identifying thresholds relevant to a particular system rather than universal standards, the steps of the framework aim to optimize the chances of delineation without imposing pre-conceived patterns onto estimates of species limits. <br/
Spatial and temporal signatures of ecological constraints on diversity
Full text linkBroad-scale diversity patterns are the outcome of ecological and evolutionary processes that
permit different numbers of species to coexist in a region. Many studies have focused on
understanding the factors that allow a region to contain more species or a clade to diversify
more rapidly. In this thesis, I shift focus to instead explore the constraints that prevent
biodiversity increasing unbounded, using a combination of phylogenetic and biogeographical
approaches across a range of temporal and spatial scales. In chapter two, I investigate
conservatism (i.e., the tendency for more closely related species to be more similar) in the
extremes of climate tolerated by a species, assessing the hypothesis that tightly-conserved
tolerances are influential in determining the range extents of the species. By using global data
from two vertebrate classes and a range of climatic variables, I assess the taxonomic
generality of this hypothesis and identify the most strongly conserved variables. In chapters
three and four, I develop novel macroecological analyses of factors that may limit the extent
of geographic ranges and apply them to Afrotropical birds (chapter three) and all continental
mammals (chapter four). Chapter five assesses how the spatial distribution of range limits can
be used to compare species’ relative abilities to occupy available landscape. In chapter six, I
present new methods to detect signals of past changes to diversity limits in phylogenies,
using simulations to explore the power of phylogenies to reveal such patterns of diversity-dependent
cladogenesis. In addition to the main research chapters, I append a synthetic
review, of which I am joint first author, exploring the evolutionary underpinnings of large-scale
species-area relationships. This thesis builds links between the macroecology of
species’ distributions with the dynamics of clades over macroevolutionary timescales to
determine how geography, phylogeny and history interact in the generation and maintenance
of large-scale biodiversity
Insect occurrence in agricultural land‐uses depends on realized niche and geographic range properties
Full text linkGeographic range size predicts species’ responses to land‐use change and intensification, but the reason why is not well established because many correlates of larger geographic ranges, such as realized niche breadth, may mediate species’ responses to environmental change. Agricultural land uses (hereafter ‘agroecosystems’) have warm, dry and more variable microclimates than do cooler and wetter mature forests, so are predicted to filter for species that have warmer, drier and broader fundamental and realized niches. To test these predictions, we estimated species’ realized niches, for temperature and precipitation, and geographic range sizes of 764 insect species by matching GBIF occurrence records to global climate layers, and modelled how species presence/absence in mature forest and nearby agroecosystems depend on species’ realized niches or geographic ranges. The predicted species niche effects consistently matched the expected direction of microclimatic transition from mature forest to agroecosystems. We found a clear signal that species with preference for warmer and drier climates were more likely to be present in agroecosystems. In addition, the probability that species occurred in different land‐use types was predicted better by species’ realized niche than their geographic range size. However, niche effects are often context‐dependent and varied amongst studies, taxonomic groups and regions used in this analysis: predicting which particular aspects of species’ realized niche cause sensitivity to land‐use change, and the underpinning mechanisms, remains a major challenge for future research and multiple components of species’ realized niches may be important to consider. Using realized niches derived from open‐source occurrence records can be a simple and widely applicable tool to help identify when biodiversity responds to the microclimate component of land‐use change
The phylogenetic structure of ecological communities under change
Full text linkDarwin first noticed that closely-related species tend to be more similar,
and that this brings them into more severe competition with
one another. In my thesis, I use information on the phylogenetic relatedness
of species to help understand the processes that structure
ecological assemblages. I start with a review of how phylogenetic
structure is useful to ecologists (chapter one), and the methodological
tools available to study it (chapter two). I then re-analyse the
Barro Colorado Island dataset, finding shifts in phylogenetic structure
across extremely fine spatial and phylogenetic scales that previously
used measures were unable to detect (chapter three). I outline a new
tool that automatically generates phylogenies for ecologists, making
use of online DNA sequence databases (chapter four). Using trait
and phylogenetic data, I examine marine benthic invertebrate assemblages
(chapter five), and characterise the structure of British birds
and butterflies (chapter six). I then prioritise British plant conservation
according to a new scheme that includes evolutionary distinctiveness,
species threat and our degree of uncertainty about species
threat (chapter seven), and conclude by considering future directions
for the study of the phylogenetic structure of ecological communities
(chapter eight)
Going Beyond Counting First Authors in Author Co-citation Analysis
Full text linkThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
- …
