Recently Formed Polyploid Plants Diversify at Lower Rates

Polyploidy, the doubling of genomic content, is a widespread feature, especially among plants, yet its macroevolutionary impacts are contentious. Traditionally, polyploidy has been considered an evolutionary dead end, whereas recent genomic studies suggest that polyploidy has been a key driver of macroevolutionary success. We examined the consequences of polyploidy on the time scale of genera across a diverse set of vascular plants, encompassing hundreds of inferred polyploidization events. Likelihood-based analyses indicate that polyploids generally exhibit lower speciation rates and higher extinction rates than diploids, providing the first quantitative corroboration of the dead-end hypothesis. The increased speciation rates of diploids can, in part, be ascribed to their capacity to speciate via polyploidy. Only particularly fit lineages of polyploids may persist to enjoy longer-term evolutionary success.

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Diversification in Monkeyflowers: An Investigation of the Effects of Elevation and Floral Color in the Genus Mimulus

International Journal of Evolutionary Biology ◽

10.1155/2014/382453 ◽

2014 ◽

Vol 2014 ◽

pp. 1-10 ◽

Cited By ~ 2

Author(s):

Ezgi Ogutcen ◽

Brooklyn Hamper ◽

Jana C. Vamosi

Keyword(s):

High Elevation ◽

Flowering Plant ◽

Floral Colour ◽

Transition Rates ◽

Extinction Rates ◽

Floral Color ◽

Speciation Rates ◽

Evolutionary Success ◽

Plant Families ◽

High Elevations

The vast diversity of floral colours in many flowering plant families, paired with the observation of preferences among pollinators, suggests that floral colour may be involved in the process of speciation in flowering plants. While transitions in floral colour have been examined in numerous genera, we have very little information on the consequences of floral colour transitions to the evolutionary success of a clade. Overlaid upon these patterns is the possibility that certain floral colours are more prevalent in certain environments, with the causes of differential diversification being more directly determined by geographical distribution. Here we examine transition rates to anthocyanin + carotenoid rich (red/orange/fuschia) flowers and examine whether red/orange flowers are associated with differences in speciation and/or extinction rates in Mimulus. Because it has been suggested that reddish flowers are more prevalent at high elevation, we also examine the macroevolutionary evidence for this association and determine if there is evidence for differential diversification at high elevations. We find that, while red/orange clades have equivalent speciation rates, the trait state of reddish flowers reverts more rapidly to the nonreddish trait state. Moreover, there is evidence for high speciation rates at high elevation and no evidence for transition rates in floral colour to differ depending on elevation.

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Evolutionarily distinct “living fossils” require both lower speciation and lower extinction rates

Paleobiology ◽

10.1017/pab.2016.36 ◽

2016 ◽

Vol 43 (1) ◽

pp. 34-48 ◽

Cited By ~ 8

Author(s):

Dominic J. Bennett ◽

Mark D. Sutton ◽

Samuel T. Turvey

Keyword(s):

Growth Model ◽

Tree Growth ◽

Phylogenetic Trees ◽

Tree Of Life ◽

Unequal Distribution ◽

Living Fossil ◽

Extinction Rates ◽

Dead End ◽

Speciation Rates ◽

Tree Growth Model

AbstractAs a label for a distinct category of life, “living fossil” is controversial. The term has multiple definitions, and it is unclear whether the label can be genuinely used to delimit biodiversity. Even taking a purely phylogenetic perspective in which a proxy for the living fossil is evolutionary distinctness (ED), an inconsistency arises: Does it refer to “dead-end” lineages doomed to extinction or “panchronic” lineages that survive through multiple epochs? Recent tree-growth model studies indicate that speciation rates must have been unequally distributed among species in the past to produce the shape of the tree of life. Although an uneven distribution of speciation rates may create the possibility for a distinct group of living fossil lineages, such a grouping could only be considered genuine if extinction rates also show a consistent pattern, be it indicative of dead-end or panchronic lineages. To determine whether extinction rates also show an unequal distribution, we developed a tree-growth model in which the probability of speciation and extinction is a function of a tip’s ED. We simulated thousands of trees in which the ED function for a tip is randomly and independently determined for speciation and extinction rates. We find that simulations in which the most evolutionarily distinct tips have lower rates of speciation and extinction produce phylogenetic trees closest in shape to empirical trees. This implies that a distinct set of lineages with reduced rates of diversification, indicative of a panchronic definition, is required to create the shape of the tree of life.

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Relocating the Dead-End

Hidden Histories of the Dead ◽

10.1017/9781108633154.001 ◽

2021 ◽

pp. 1-100

Keyword(s):

Dead End ◽

The Dead

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Geographic contingency, not species sorting, dominates macroevolutionary dynamics in an extinct clade of neogastropods (Volutospina; Volutidae)

Paleobiology ◽

10.1017/pab.2020.60 ◽

2021 ◽

pp. 1-15

Author(s):

Dana S. Friend ◽

Brendan M. Anderson ◽

Warren D. Allmon

Keyword(s):

Middle Eocene ◽

Ecological Factors ◽

Geographic Range ◽

Late Eocene ◽

Range Size ◽

Species Sorting ◽

Extinction Rates ◽

Geographic Range Size ◽

Speciation Rates ◽

Planktotrophic Larvae

Abstract Rates of speciation and extinction are often linked to many ecological factors, traits (emergent and nonemergent) such as environmental tolerance, body size, feeding type, and geographic range. Marine gastropods in particular have been used to examine the role of larval dispersal in speciation. However, relatively few studies have been conducted placing larval modes in species-level phylogenetic context. Those that have, have not incorporated fossil data, while landmark macroevolutionary studies on fossil clades have not considered both phylogenetic context and net speciation (speciation–extinction) rates. This study utilizes Eocene volutid Volutospina species from the U.S. Gulf Coastal Plain and the Hampshire Basin, U.K., to explore the relationships among larval mode, geographic range, and duration. Based on the phylogeny of these Volutospina, we calculated speciation and extinction rates in order to compare the macroevolutionary effects of larval mode. Species with planktotrophic larvae had a median duration of 9.7 Myr, which compared significantly to 4.7 Myr for those with non-planktotrophic larvae. Larval mode did not significantly factor into geographic-range size, but U.S. and U.K. species do differ, indicating a locality-specific component to maximum geographic-range size. Non-planktotrophs (NPTs)were absent among the Volutospina species during the Paleocene–early Eocene. The relative proportions of NPTs increased in the early middle Eocene, and the late Eocene was characterized by disappearance of planktotrophs (PTs). The pattern of observed lineage diversity shows an increasing preponderance of NPTs; however, this is clearly driven by a dramatic extinction of PTs, rather than higher NPT speciation rates during the late Eocene. This study adds nuance to paleontology's understanding of the macroevolutionary consequences of larval mode.

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Metalloregulator CueR biases RNA polymerase’s kinetic sampling of dead-end or open complex to repress or activate transcription

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1515231112 ◽

2015 ◽

Vol 112 (44) ◽

pp. 13467-13472 ◽

Cited By ~ 13

Author(s):

Danya J. Martell ◽

Chandra P. Joshi ◽

Ahmed Gaballa ◽

Ace George Santiago ◽

Tai-Yen Chen ◽

...

Keyword(s):

Single Molecule ◽

Transcription Initiation ◽

Structural Changes ◽

Dynamic Equilibrium ◽

Specific Binding ◽

Binding Mode ◽

Biased Sampling ◽

Single Molecule Fret ◽

Dead End ◽

The Dead

Metalloregulators respond to metal ions to regulate transcription of metal homeostasis genes. MerR-family metalloregulators act on σ70-dependent suboptimal promoters and operate via a unique DNA distortion mechanism in which both the apo and holo forms of the regulators bind tightly to their operator sequence, distorting DNA structure and leading to transcription repression or activation, respectively. It remains unclear how these metalloregulator−DNA interactions are coupled dynamically to RNA polymerase (RNAP) interactions with DNA for transcription regulation. Using single-molecule FRET, we study how the copper efflux regulator (CueR)—a Cu+-responsive MerR-family metalloregulator—modulates RNAP interactions with CueR’s cognate suboptimal promoter PcopA, and how RNAP affects CueR−PcopAinteractions. We find that RNAP can form two noninterconverting complexes at PcopAin the absence of nucleotides: a dead-end complex and an open complex, constituting a branched interaction pathway that is distinct from the linear pathway prevalent for transcription initiation at optimal promoters. Capitalizing on this branched pathway, CueR operates via a “biased sampling” instead of “dynamic equilibrium shifting” mechanism in regulating transcription initiation; it modulates RNAP’s binding–unbinding kinetics, without allowing interconversions between the dead-end and open complexes. Instead, the apo-repressor form reinforces the dominance of the dead-end complex to repress transcription, and the holo-activator form shifts the interactions toward the open complex to activate transcription. RNAP, in turn, locks CueR binding at PcopAinto its specific binding mode, likely helping amplify the differences between apo- and holo-CueR in imposing DNA structural changes. Therefore, RNAP and CueR work synergistically in regulating transcription.

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Effect of Disruption Methods on the Dead-End Microfiltration Behavior of Yeast Suspension

Separation Science and Technology ◽

10.1080/01496391003727890 ◽

2010 ◽

Vol 45 (8) ◽

pp. 1042-1050 ◽

Cited By ~ 9

Author(s):

Dan Liu ◽

Raphaëlle Savoire ◽

Eugène Vorobiev ◽

Jean-Louis Lanoisellé

Keyword(s):

Yeast Suspension ◽

Dead End ◽

The Dead

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Reconciliation ecology and the future of species diversity

Oryx ◽

10.1017/s0030605303000371 ◽

2003 ◽

Vol 37 (2) ◽

pp. 194-205 ◽

Cited By ~ 220

Author(s):

Michael L. Rosenzweig

Keyword(s):

Steady State ◽

Species Diversity ◽

Natural Area ◽

Reconciliation Ecology ◽

Anthropogenic Habitats ◽

Extinction Rates ◽

Broad Array ◽

Speciation Rates ◽

Species Area ◽

Biogeographical Province

Species-area relationships (SPARs) dictate a sea change in the strategies of biodiversity conservation. SPARs exist at three ecological scales: Sample-area SPARs (a larger area within a biogeographical province will tend to include more habitat types, and thus more species, than a smaller one), Archipelagic SPARs (the islands of an archipelago show SPARs that combine the habitat-sampling process with the problem of dispersal to an island), and Interprovincial SPARs (other things being equal, the speciation rates of larger biogeographical provinces are higher and their extinction rates are lower, leading to diversities in proportion to provincial area). SPARs are the products of steady-state dynamics in diversity, and such dynamics appears to have characterized the earth for most of the last 500 million years. As people reduce the area available to wild species, they impose a linear reduction of the earth's species diversity that will follow the largest of these scales, i.e. each 1% reduction of natural area will cost about 1% of steady-state diversity. Reserving small tracts of wild habitat can only delay these reductions. But we can stop most of them by redesigning anthropogenic habitats so that their use is compatible with use by a broad array of other species. That is reconciliation ecology. Many pilot projects, whether intentionally or inadvertently espousing reconciliation ecology, are demonstrating that it can be done.

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