scholarly journals Memory in trait macroevolution

2018 ◽  
Author(s):  
Emma E. Goldberg ◽  
Jasmine Foo
Keyword(s):  
Markov Model ◽  
Renewal Process ◽  
Evolutionary Trajectory ◽  
Trait Evolution ◽  
Comparative Tests ◽  
Surface Transition ◽  
History Of ◽  
Tests Of Hypotheses ◽  
Cave Dweller ◽  
Surface Environment

AbstractThe history of a trait within a lineage may influence its future evolutionary trajectory, but macroevolutionary theory of this process is not well developed. For example, consider the simple binary trait of living in cave versus surface habitat. The longer a species has been cave-dwelling, the more may accumulated loss of vision, pigmentation, and defense restrict future adaptation if the species encounters the surface environment. However, the Markov model of discrete trait evolution that is widely adopted in phylogenetics does not allow the rate of cave-to-surface transition to decrease with longer duration as a cave-dweller. Here, we describe three models of evolution that remove this ‘memory-less’ constraint, using a renewal process to generalize beyond the typical Poisson process of discrete trait macroevolution. We then show how the two-state renewal process can be used for inference, and we investigate the potential of phylogenetic comparative data to reveal different influences of trait duration, or ‘memory’ in trait evolution. We hope that such approaches may open new avenues for modeling trait evolution and for broad comparative tests of hypotheses that some traits become entrenched.

New Zealand translocations: theory and practice

1995 ◽  
Vol 2 (1) ◽  
pp. 39 ◽  
Author(s):  
Doug P. Armstong ◽  
Ian G. McLean
Keyword(s):  
Population Dynamics ◽  
New Zealand ◽  
Experimental Tests ◽  
Theory And Practice ◽  
Habitat Requirements ◽  
Metapopulation Dynamics ◽  
Behavioural Adaptation ◽  
New Locations ◽  
History Of ◽  
Tests Of Hypotheses

One of the most common tools in New Zealand conservation is to translocate species to new locations. There have now been over 400 translocations done for conservation reasons, mainly involving terrestrial birds. Most translocations have been done strictly as management exercises, with little or no reference to theory. Nevertheless, translocations always involve some underlying theory, given that people must inevitably choose among a range of potential translocation strategies. We review theory relevant to translocations in the following areas: habitat requirements, susceptibility to predation, behavioural adaptation, population dynamics, genetics, metapopulation dynamics, and community ecology. For each area we review and evaluate the models that seem to underpin translocation strategies used in New Zealand. We report experiments testing some of these models, but note that theory underlying translocation strategies is largely untested despite a long history of translocations. We conclude by suggesting key areas for research, both theoretical and empirical. We particularly recommend that translocations be designed as experimental tests of hypotheses whenever possible.

A Markov Model of the Natural History of Multiple Sclerosis

1985 ◽  
Vol 4 (4) ◽  
pp. 227-239 ◽  
Author(s):  
Christina Wolfson ◽  
Christian Confavreux
Keyword(s):  
Multiple Sclerosis ◽  
Natural History ◽  
Markov Model ◽  
History Of

scholarly journals A Markov model of urban evolution: Neighbourhood change as a complex process

PLoS ONE ◽  
2021 ◽  
Vol 16 (1) ◽  
pp. e0245357
Author(s):  
Daniel Silver ◽  
Thiago H. Silva
Keyword(s):  
Markov Model ◽  
Markov Models ◽  
Past Research ◽  
Hierarchical Approach ◽  
Evolutionary Trajectory ◽  
Complex Process ◽  
Trajectories Of Change ◽  
Neighbourhood Change ◽  
The Impact ◽  
Complexity Theories

This paper seeks to advance neighbourhood change research and complexity theories of cities by developing and exploring a Markov model of socio-spatial neighbourhood evolution in Toronto, Canada. First, we classify Toronto neighbourhoods into distinct groups using established geodemographic segmentation techniques, a relatively novel application in this geographic setting. Extending previous studies, we pursue a hierarchical approach to classifying neighbourhoods that situates many neighbourhood types within the city’s broader structure. Our hierarchical approach is able to incorporate a richer set of types than most past research and allows us to study how neighbourhoods’ positions within this hierarchy shape their trajectories of change. Second, we use Markov models to identify generative processes that produce patterns of change in the city’s distribution of neighbourhood types. Moreover, we add a spatial component to the Markov process to uncover the extent to which change in one type of neighbourhood depends on the character of nearby neighbourhoods. In contrast to the few studies that have explored Markov models in this research tradition, we validate the model’s predictive power. Third, we demonstrate how to use such models in theoretical scenarios considering the impact on the city’s predicted evolutionary trajectory when existing probabilities of neighbourhood transitions or distributions of neighbourhood types would hypothetically change. Markov models of transition patterns prove to be highly accurate in predicting the final distribution of neighbourhood types. Counterfactual scenarios empirically demonstrate urban complexity: small initial changes reverberate throughout the system, and unfold differently depending on their initial geographic distribution. These scenarios show the value of complexity as a framework for interpreting data and guiding scenario-based planning exercises.

Ancient Meteorite Finds and the Earth's Surface Environment

2000 ◽  
Vol 53 (2) ◽  
pp. 131-142 ◽  
Author(s):  
Philip A. Bland ◽  
Alex W. R. Bevan ◽  
A. J. Tim Jull
Keyword(s):  
Age Distribution ◽  
Cosmogenic Radionuclides ◽  
Cold Desert ◽  
Frequency Distributions ◽  
Carbon Isotopic ◽  
The Earth ◽  
History Of ◽  
Tropical Areas ◽  
Surface Environment ◽  
Terrestrial Age

AbstractThe flux of meteorites to the Earth over the last 50,000 yr has remained approximately constant. Most meteorites that fall in temperate or tropical areas are destroyed on a time scale which is short compared to the rate of infall; however, in arid regions (both “hot” deserts and the “cold” desert of Antarctica) weathering is slower and accumulations of meteorites may occur. The initial composition for many meteorite groups is well known from modern falls, and terrestrial ages may be established from analyses of the abundance of cosmogenic radionuclides, providing an absolute chronology for recording terrestrial processes. As samples are falling constantly, and are distributed approximately evenly over the Earth, meteorites may thus be thought of as an appropriate “standard sample” for studying aspects of the terrestrial surface environment. Studies involving 14C and 36Cl terrestrial ages of meteorites, 57Fe Mössbauer spectroscopy (to quantify the degree of oxidation in samples), stable isotopes, and determination of halogen abundances are yielding information on the terrestrial history of meteorites: (i) terrestrial age and oxidation-frequency distributions for populations of samples allow the ages of surfaces to be estimated; (ii) differences in the weathering rate of samples between sites allows constraints to be imposed on the effect of climate on rock weathering rates; (iii) carbon isotopic compositions of generations of carbonate growth within meteorites allows, in some cases, temperatures of formation of carbonates to be estimated; (iv) structure in the oxidation–terrestrial age distribution for meteorites from some arid accumulation sites (specifically, the Nullarbor of Australia) appears to be linked to previous humid/arid cycles; (v) meteorite accumulations in Antarctica have been used to constrain aspects of the Quaternary evolution of the ice sheet, and terrestrial age and oxidation data have been used to constrain ice flow.

scholarly journals Population genomic analyses reveal a history of range expansion and trait evolution across the native and invaded range of yellow starthistle (Centaurea solstitialis)

2017 ◽  
Vol 26 (4) ◽  
pp. 1131-1147 ◽  
Author(s):  
Brittany S. Barker ◽  
Krikor Andonian ◽  
Sarah M. Swope ◽  
Douglas G. Luster ◽  
Katrina M. Dlugosch
Keyword(s):  
Range Expansion ◽  
Centaurea Solstitialis ◽  
Yellow Starthistle ◽  
Trait Evolution ◽  
Population Genomic ◽  
Genomic Analyses ◽  
History Of

scholarly journals Viruses Infecting a Freshwater Filamentous Cyanobacterium (Nostocsp.) Encode a Functional CRISPR Array and a Proteobacterial DNA Polymerase B

mBio ◽  
2016 ◽  
Vol 7 (3) ◽  
Author(s):  
Caroline Chénard ◽  
Jennifer F. Wirth ◽  
Curtis A. Suttle
Keyword(s):  
Dna Polymerase ◽  
Evolutionary History ◽  
Genomic Analysis ◽  
Open Reading Frames ◽  
Filamentous Cyanobacterium ◽  
Filamentous Cyanobacteria ◽  
Evolutionary Trajectory ◽  
Crispr Array ◽  
History Of ◽  
Pcc 7120

ABSTRACT  Here we present the first genomic characterization of viruses infectingNostoc, a genus of ecologically important cyanobacteria that are widespread in freshwater. Cyanophages A-1 and N-1 were isolated in the 1970s and infectNostocsp. strain PCC 7210 but remained genomically uncharacterized. Their 68,304- and 64,960-bp genomes are strikingly different from those of other sequenced cyanophages. Many putative genes that code for proteins with known functions are similar to those found in filamentous cyanobacteria, showing a long evolutionary history in their host. Cyanophage N-1 encodes a CRISPR array that is transcribed during infection and is similar to the DR5 family of CRISPRs commonly found in cyanobacteria. The presence of a host-related CRISPR array in a cyanophage suggests that the phage can transfer the CRISPR among related cyanobacteria and thereby provide resistance to infection with competing phages. Both viruses also encode a distinct DNA polymerase B that is closely related to those found in plasmids ofCyanothecesp. strain PCC 7424,Nostocsp. strain PCC 7120, andAnabaena variabilisATCC 29413. These polymerases form a distinct evolutionary group that is more closely related to DNA polymerases of proteobacteria than to those of other viruses. This suggests that the polymerase was acquired from a proteobacterium by an ancestral virus and transferred to the cyanobacterial plasmid. Many other open reading frames are similar to a prophage-like element in the genome ofNostocsp. strain PCC 7524. TheNostoccyanophages reveal a history of gene transfers between filamentous cyanobacteria and their viruses that have helped to forge the evolutionary trajectory of this previously unrecognized group of phages.IMPORTANCEFilamentous cyanobacteria belonging to the genusNostocare widespread and ecologically important in freshwater, yet little is known about the genomic content of their viruses. Here we report the first genomic analysis of cyanophages infecting filamentous freshwater cyanobacteria, revealing that their gene content is unlike that of other cyanophages. In addition to sharing many gene homologues with freshwater cyanobacteria, cyanophage N-1 encodes a CRISPR array and expresses it upon infection. Also, both viruses contain a DNA polymerase B-encoding gene with high similarity to genes found in proteobacterial plasmids of filamentous cyanobacteria. The observation that phages can acquire CRISPRs from their hosts suggests that phages can also move them among hosts, thereby conferring resistance to competing phages. The presence in these cyanophages of CRISPR and DNA polymerase B sequences, as well as a suite of other host-related genes, illustrates the long and complex evolutionary history of these viruses and their hosts.

scholarly journals Rapid phenotypic evolution following shifts in life cycle complexity

2018 ◽  
Vol 285 (1871) ◽  
pp. 20172304 ◽  
Author(s):  
Ronald M. Bonett ◽  
John G. Phillips ◽  
Nicholus M. Ledbetter ◽  
Samuel D. Martin ◽  
Luke Lehman
Keyword(s):  
Life Cycle ◽  
Vertebral Column ◽  
Life Stages ◽  
Phenotypic Evolution ◽  
Trait Evolution ◽  
Life Cycle Stages ◽  
Biphasic Life Cycle ◽  
History Of ◽  
Life Cycle Evolution

Life cycle strategies have evolved extensively throughout the history of metazoans. The expression of disparate life stages within a single ontogeny can present conflicts to trait evolution, and therefore may have played a major role in shaping metazoan forms. However, few studies have examined the consequences of adding or subtracting life stages on patterns of trait evolution. By analysing trait evolution in a clade of closely related salamander lineages we show that shifts in the number of life cycle stages are associated with rapid phenotypic evolution. Specifically, salamanders with an aquatic-only (paedomorphic) life cycle have frequently added vertebrae to their trunk skeleton compared with closely related lineages with a complex aquatic-to-terrestrial (biphasic) life cycle. The rate of vertebral column evolution is also substantially lower in biphasic lineages, which may reflect the functional compromise of a complex cycle. This study demonstrates that the consequences of life cycle evolution can be detected at very fine scales of divergence. Rapid evolutionary responses can result from shifts in selective regimes following changes in life cycle complexity.

scholarly journals Transitions between foot postures are associated with elevated rates of body size evolution in mammals

2019 ◽  
Vol 116 (7) ◽  
pp. 2618-2623 ◽  
Author(s):  
Tai Kubo ◽  
Manabu Sakamoto ◽  
Andrew Meade ◽  
Chris Venditti
Keyword(s):  
Body Size ◽  
Mammalian Species ◽  
Evolutionary Trajectory ◽  
Future Studies ◽  
Terrestrial Mammals ◽  
Size Evolution ◽  
Foot Posture ◽  
History Of ◽  
The Common ◽  
Body Size Evolution

Terrestrial mammals have evolved various foot postures: flat-footed (plantigrady), tiptoed (digitigrady), and hooved (unguligrady) postures. Although the importance of foot posture on ecology and body size of mammalian species has been widely recognized, its evolutionary trajectory and influence on body size evolution across mammalian phylogeny remain untested. Taking a Bayesian phylogenetic approach combined with a comprehensive dataset of foot postures in 880 extant mammalian species, we investigated the evolutionary history of foot postures and rates of body size evolution, within the same posture and at transitions between postures. Our results show that the common ancestor of mammals was plantigrade, and transitions predominantly occurred only between plantigrady and digitigrady and between digitigrady and unguligrady. At the transitions between plantigrady and digitigrady and between digitigrady and unguligrady, rates of body size evolution are significantly elevated leading to the larger body masses of digitigrade species (∼1 kg) and unguligrade species (∼78 kg) compared with their respective ancestral postures [plantigrady (∼0.75 kg) and digitigrady]. Our results demonstrate the importance of foot postures on mammalian body size evolution and have implications for mammalian body size increase through time. In addition, we highlight a way forward for future studies that seek to integrate morphofunctional and macroevolutionary approaches.

scholarly journals Selection is stronger in early-versus-late stages of divergence in a Neotropical livebearing fish

2016 ◽  
Vol 12 (3) ◽  
pp. 20151022 ◽  
Author(s):  
Spencer J. Ingley ◽  
Jerald B. Johnson
Keyword(s):  
Life History ◽  
Life History Traits ◽  
Single Point ◽  
Evolutionary Trajectory ◽  
Trait Evolution ◽  
The Difference ◽  
Livebearing Fish ◽  
Late Stages ◽  
Over Time

How selection acts to drive trait evolution at different stages of divergence is of fundamental importance in our understanding of the origins of biodiversity. Yet, most studies have focused on a single point along an evolutionary trajectory. Here, we provide a case study evaluating the strength of divergent selection acting on life-history traits at early-versus-late stages of divergence in Brachyrhaphis fishes. We find that the difference in selection is stronger in the early-diverged population than the late-diverged population, and that trait differences acquired early are maintained over time.

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