Testing reduced evolutionary rates during the Late Palaeozoic Ice Age using the crinoid fossil record

In 2003, Stanley & Powell reported depressed rates of origination and extinction in marine invertebrates during the Late Palaeozoic Ice Age (LPIA). Using a database of crinoid genera, rates of origination, extinction and genus duration were calculated at the stage level from the Early Devonian to the Late Permian. This 165 m.y. time span includes non‐glacial intervals before and after the LPIA, which spanned the Serpukhovian to Sakmarian, providing background rates for comparison. Data generated on crinoid evolutionary rates during the Middle to Late Palaeozoic were analysed and compared to Stanley & Powell's data to determine whether crinoid evolutionary patterns support their findings or suggest an alternative hypothesis. Rates of origination and extinction in all crinoid clades were reduced during the LPIA compared to the combined background intervals before and after the LPIA. However, crinoid diversity was higher during the LPIA than the surrounding time intervals. The difference in diversity trends between crinoids and other marine invertebrates is due to the advanced cladids clade. Unstable, fluctuating environmental conditions during the LPIA may have created habitats suitable for opportunistic crinoid genera that reduced both the probability of origination and extinction. The increased diversity of the advanced cladids is likely due to their unique adaptation of muscular arm articulations, which allowed them to thrive in marine settings with increased siliciclastic influx brought on by the Alleghenian orogeny. Despite the advanced cladids’ departure from the expected diversity count, the results of analyses performed on the updated crinoid database provide independent confirmation of Stanley & Powell's original hypothesis of depressed evolutionary rates in marine invertebrates during the LPIA.     

Evolutionary dynamics of taxonomic structure

The distribution of species among genera and higher taxa has largely untapped potential to reveal among-clade variation in rates of origination and extinction. The probability distribution of the number of species within a genus is modelled with a stochastic, time-homogeneous birth-death model having two parameters: the rate of species extinction, μ, and the rate of genus origination, γ, each scaled as a multiple of the rate of within-genus speciation, λ. The distribution is more sensitive to γ than to μ, although μ affects the size of the largest genera. The species : genus ratio depends strongly on both γ and μ, and so is not a good diagnostic of evolutionary dynamics. The proportion of monotypic genera, however, depends mainly on γ, and so may provide an index of the genus origination rate. Application to living marine molluscs of New Zealand shows that bivalves have a higher relative rate of genus origination than gastropods. This is supported by the analysis of palaeontological data. This concordance suggests that analysis of living taxonomic distributions may allow inference of macroevolutionary dynamics even without a fossil record.     

Phylogenetic Clustering of Origination and Extinction across the Late Ordovician Mass Extinction

Mass extinctions can have dramatic effects on the trajectory of life, but in some cases the effects can be relatively small even when extinction rates are high. For example, the Late Ordovician mass extinction is the second most severe in terms of the proportion of genera eliminated, yet is noted for the lack of ecological consequences and shifts in clade dominance. By comparison, the end-Cretaceous mass extinction was less severe but eliminated several major clades while some rare surviving clades diversified in the Paleogene. This disconnect may be better understood by incorporating the phylogenetic relatedness of taxa into studies of mass extinctions, as the factors driving extinction and recovery are thought to be phylogenetically conserved and should therefore promote both origination and extinction of closely related taxa. Here, we test whether there was phylogenetic selectivity in extinction and origination using brachiopod genera from the Middle Ordovician through the Devonian. Using an index of taxonomic clustering (R_CL) as a proxy for phylogenetic clustering, we find that A) both extinctions and originations shift from taxonomically random or weakly clustered within families in the Ordovician to strongly clustered in the Silurian and Devonian, beginning with the recovery following the Late Ordovician mass extinction, and B) the Late Ordovician mass extinction was itself only weakly clustered. Both results stand in stark contrast to Cretaceous-Cenozoic bivalves, which showed significant levels of taxonomic clustering of extinctions in the Cretaceous, including strong clustering in the mass extinction, but taxonomically random extinctions in the Cenozoic. The contrasting patterns between the Late Ordovician and end-Cretaceous events suggest a complex relationship between the phylogenetic selectivity of mass extinctions and the long-term phylogenetic signal in origination and extinction patterns.     

Considering the case for biodiversity cycles: re-examining the evidence for periodicity in the fossil record

We re-examine the evidence for a 62 million year (Myr) periodicity in biodiversity throughout the Phanerozoic history of animal life reported by, as well as related questions of periodicity in origination and extinction. We find that the signal is robust against variations in methods of analysis, and is based on fluctuations in the Paleozoic and a substantial part of the Mesozoic. Examination of origination and extinction is somewhat ambiguous, with results depending upon procedure. Origination and extinction intensity as defined by may be affected by an artifact at 27 Myr in the duration of stratigraphic intervals. Nevertheless, when a procedure free of this artifact is implemented, the 27 Myr periodicity appears in origination, suggesting that the artifact may ultimately be based on a signal in the data. A 62 Myr feature appears in extinction, when this same procedure is used. We conclude that evidence for a periodicity at 62 Myr is robust, and evidence for periodicity at approximately 27 Myr is also present, albeit more ambiguous.     

Correlations in fossil extinction and origination rates through geological time

Recent analyses have suggested that extinction and origination rates exhibit long-range correlations, implying that the fossil record may be controlled by self-organized criticality or other scale-free internal dynamics of the biosphere. Here we directly test for correlations in the fossil record by calculating the autocorrelation of extinction [corrected] and origination rates through time. Our results show that extinction rates are uncorrelated beyond the average duration of a stratigraphic interval. Thus, they lack the long-range correlations predicted by the self-organized criticality hypothesis. In contrast, origination rates show strong autocorrelations due to long-term trends. After detrending, origination rates generally show weak positive correlations at lags of 5-10 million years (Myr) and weak negative correlations at lags of 10-30 Myr, consistent with aperiodic oscillations around their long-term trends. We hypothesize that origination rates are more correlated than extinction rates because originations of new taxa create new ecological niches and new evolutionary pathways for reaching them, thus creating conditions that favour further diversification.     

Genetic management of captive populations: the advantages of circular mating

We performed computer simulations to evaluate the effectiveness of circular mating as a genetic management option for captive populations. As a benchmark, we used the method proposed by Fernández and Caballero according to which parental contributions are set to produce minimum coancestry among the offspring and matings are performed so as to minimize mean pairwise coancestry (referred to as the Gc/mc method). In contrast to other methods, fitness does not vary with population size in the case of circular mating, and can be higher than under random mating. Whether circular mating is an effective method in conserving captive populations depends on the trade-off between different considerations. On the one hand, circular mating shows the highest allelic diversity and the lowest mean pairwise coancestry for all population sizes. It also shows a relatively higher efficiency of purging deleterious alleles. More importantly, circular mating can significantly increase the success probability of populations released to the wild relative to the Gc/mc method. On the other hand, circular mating has the drawback of showing high inbreeding rates and low fitness in early generations, which can result to an increase in the extinction probability of the captive populations. However, this increase is slight unless population size and litter size are both very low. Overall, if the slight increase in extinction probability can be tolerated then circular mating fulfils the primary goals of a captive breeding program, i.e., it maintains high levels of genetic diversity and increases the success probability of reintroduced populations.     

Regional patterns of evolutionary turnover in Neogene coral reefs from the central Indo-West Pacific Ocean

The Indo-Pacific is an area of intense ecological interest, not least because of the region’s rich biodiversity. Important insights into the origins, evolutionary history, and maintenance of Indo-Pacific reef faunas depend upon the analysis of faunal occurrences derived from detailed stratigraphic sections. We investigated Neogene origination and extinction patterns derived from a combination of new coral occurrences and previously published records from the central Indo-West Pacific Ocean (cIWP, Indonesia, Papua New Guinea and Fiji). Two faunal turnover events were observed. In the first, an increase in generic richness of Scleractinia from the cIWP during the middle Miocene (17–14 Ma) coincided with both large-scale sea level fluctuations and the great Mid-Miocene collision event. We raise the hypothesis that Mid-Miocene origination was facilitated by habitat and population fragmentation associated with tectonism and sea level fall. The second, subsequent, turnover event was characterized by an overall lowering of generic diversity throughout the late Miocene and Pliocene (7–3 Ma), and was followed by a pronounced pulse of extinction at the Pliocene–Pleistocene boundary (~2.6 Ma). With the exception of the onset of Pleistocene sea-level cycles and the onset of northern hemisphere glaciation around 2.5 Ma, which might explain increased extinction during this time interval, there are no tectonic, eustatic, climatic or oceanographic events that neatly coincide with this second episode of Neogene coral taxonomic turnover. Our results reveal a total of 62 genera, including synonyms, from the Miocene to the Pleistocene. Neither episode of turnover among coral genera is exactly coincident with turnover in the Atlantic thus regional environmental change is found to drive Neogene reef dynamics.     

Extinction risk assessment of declining wild populations: The case of the southern Bluefin Tuna

We estimate the extinction probability of a large and decreasing population, the southern bluefin tuna. This tuna was listed as critically endangered by the World Conservation Union (IUCN) in 1996. However, the absolute population size is still large and the extinction probability within the next half century is negligible if the recent population decline rate does not increase in the future. IUCN’s criterion with respect to the population decline rate should be linked to the absolute population size, if this is estimated. Several methods estimating the probability of extinction conclude that the southern bluefin tuna population will be below 500 mature individuals within the next 100 years and may be listed as vulnerable. These analyses suggest that extinction risk assessment is useful for management action for taxa that still have large population and are rapidly decreasing.     

Exploring the major depletions of conodont diversity during the Triassic

In this paper, we show that the Triassic fossil record reflects just two great depletions of conodont diversity before the Rhaetian, which occurred in the Smithian (Olenekian, Early Triassic) and in the Julian (Carnian, Late Triassic). By exploring this context, our results highlighted that they respond to different origination–extinction dynamics. Thus, while the Smithian diversity depletion can be interpreted as a consequence of elevated extinction, the Julian diversity depletion was triggered by fluctuations in origination regime. This evidence suggests that, despite the role of extinction on diversity losses, conodonts suffered crucial changes on the origination regimes during the Late Triassic which triggered these events. Notwithstanding, our results indicate that the end-Triassic diversity depletion of conodonts was produced by background extinction levels in a context of lower origination. This suggests that several biological factors, rather than a unique, environmental and/or cyclic cause, could have influenced the evolutionary history of conodonts during the Triassic.     

Pushed beyond the brink: Allee effects,environmental stochasticity,and extinction

To understand the interplay between environmental stochasticity and Allee effects, we analyse persistence, asymptotic extinction, and conditional persistence for stochastic difference equations. Our analysis reveals that persistence requires that the geometric mean of fitness at low densities is greater than one. When this geometric mean is less than one, asymptotic extinction occurs with high probability for low initial population densities. Additionally, if the population only experiences positive density-dependent feedbacks, conditional persistence occurs provided the geometric mean of fitness at high population densities is greater than one. However, if the population experiences both positive and negative density-dependent feedbacks, conditional persistence only occurs if environmental fluctuations are sufficiently small. We illustrate counter-intuitively that environmental fluctuations can increase the probability of persistence when populations are initially at low densities, and can cause asymptotic extinction of populations experiencing intermediate predation rates despite conditional persistence occurring at higher predation rates.     

The Early Origin of the Antarctic Marine Fauna and Its Evolutionary Implications

The extensive Late Cretaceous – Early Paleogene sedimentary succession of Seymour Island, N.E. Antarctic Peninsula offers an unparalleled opportunity to examine the evolutionary origins of a modern polar marine fauna. Some 38 modern Southern Ocean molluscan genera (26 gastropods and 12 bivalves), representing approximately 18% of the total modern benthic molluscan fauna, can now be traced back through at least part of this sequence. As noted elsewhere in the world, the balance of the molluscan fauna changes sharply across the Cretaceous – Paleogene (K/Pg) boundary, with gastropods subsequently becoming more diverse than bivalves. A major reason for this is a significant radiation of the Neogastropoda, which today forms one of the most diverse clades in the sea. Buccinoidea is the dominant neogastropod superfamily in both the Paleocene Sobral Formation (SF) (56% of neogastropod genera) and Early - Middle Eocene La Meseta Formation (LMF) (47%), with the Conoidea (25%) being prominent for the first time in the latter. This radiation of Neogastropoda is linked to a significant pulse of global warming that reached at least 65°S, and terminates abruptly in the upper LMF in an extinction event that most likely heralds the onset of global cooling. It is also possible that the marked Early Paleogene expansion of neogastropods in Antarctica is in part due to a global increase in rates of origination following the K/Pg mass extinction event. The radiation of this and other clades at ∼65°S indicates that Antarctica was not necessarily an evolutionary refugium, or sink, in the Early – Middle Eocene. Evolutionary source – sink dynamics may have been significantly different between the Paleogene greenhouse and Neogene icehouse worlds.     

Temporal increase in mtDNA diversity in a declining population

In small and declining populations levels of genetic variability are expected to be reduced due to effects of inbreeding and random genetic drift. As a result, both individual fitness and populations’ adaptability can be compromised, and the probability of extinction increased. Therefore, maintenance of genetic variability is a crucial goal in conservation biology. Here we show that although the level of genetic variability in mtDNA of the endangered Fennoscandian lesser white‐fronted goose Anser erythropus population is currently lower than in the neigbouring populations, it has increased six‐fold during the past 140 years despite the precipitously declining population. The explanation for increased genetic diversity in Fennoscandia appears to be recent spontaneous increase in male immigration rate equalling 0.56 per generation. This inference is supported by data on nuclear microsatellite markers, the latter of which show that the current and the historical Fennoscandian populations are significantly differentiated (F_ST = 0.046, P = 0) due to changes in allele frequencies. The effect of male‐mediated gene flow is potentially dichotomous. On the one hand it may rescue the Fennoscandian lesser white‐fronted goose from loss of genetic variability, but on the other hand, it eradicates the original genetic characteristics of this population.     

Interplay of Darwinian and frequency-dependent selection in the host-associated microbial populations

In order to analyze the microevolutionary processes in host-associated microorganisms, we simulated the dynamics of rhizobia populations composed of a parental strain and its mutants possessing the altered fitness within "plant-soil" system. The population dynamics was presented as a series of cycles (each one involves "soil-->rhizosphere-->nodules-->soil" succession) described using recurrent equations. For representing the selection and mutation pressures, we used a universal approach based on calculating the shifts in the genetic ratios of competing bacterial genotypes within the particular habitats and across several habitats. Analysis of the model demonstrated that a balanced polymorphism may be established in rhizobia population: mutants with an improved fitness do not supplant completely the parental strain while mutants with a decreased fitness may be maintained stably. This polymorphism is caused by a rescue of low-fitted genotypes via negative frequency-dependent selection (FDS) that is implemented during inoculation of nodules and balances the Darwinian selection that occurs during multiplication or extinction of bacteria at different habitats. The most diverse populations are formed if the rhizobia are equally successful in soil and nodules, while a marked preference for any of these habitats results in the decrease of diversity. Our simulation suggests that FDS can maintain the mutualistic rhizobia-legume interactions under the stress conditions deleterious for surviving the bacterial strains capable for intensive N2 fixation. Genetic consequences of releasing the modified rhizobia strains may be addressed using the presented model.     

Did hard substrate taxa diversify prior to the Great Ordovician Biodiversification Event?

The Great Ordovician Biodiversification Event (GOBE) refers to one of the greatest increases in biodiversity during the Phanerozoic. Recent studies have shown that this taxonomic increase can be attributed to elevated origination rates around the Dapingian–Darriwilian boundary in the Middle Ordovician, while extinction rates stayed relatively constant throughout the Ordovician. Even though this global pattern of origination and extinction appears similar across diverse groups and geographical areas, earlier studies suggested that hard substrate taxa may have diversified prior to the GOBE, during the Early Ordovician. Here, we quantify Ordovician diversification dynamics of hard substrate taxa while simultaneously accounting for temporally varying sampling probabilities. Diversification rates of hard substrate taxa, both as a whole and when analysed as separate groups, appear to be very similar to those of free-living benthic taxa. The observation that the diversification dynamics of many different taxonomic and ecological groups show the same temporal pattern, suggests a common cause of Ordovician diversification dynamics.     

An empirical test of the bet‐hedging polyandry hypothesis: Female red flour beetles avoid extinction via multiple mating

Bet‐hedging via polyandry (spreading the extinction risk of the female''s lineage over multiple males) may explain the evolution of female multiple mating, which is found in a wide range of animal and plant taxa. This hypothesis posits that females can increase their fitness via polyandrous mating when “unsuitable” males (i.e., males causing reproductive failure for various reasons) are frequent in the population and females cannot discriminate such unsuitable mates. Although recent theoretical studies have shown that polyandry can operate as a bet‐hedging strategy, empirical tests are scarce. In the present study, we tested the bet‐hedging polyandry hypothesis by using the red flour beetle Tribolium castaneum. We compared female reproductive success between monandry and polyandry treatments when females mated with males randomly collected from an experimental population, including 20% irradiated (infertile) males. In addition, we evaluated geometric mean fitness across multiple generations as the index of adaptability of bet‐hedging traits. Polyandrous females showed a significantly higher egg hatching rate and higher geometric mean fitness than monandrous females. These results strongly support the bet‐hedging polyandry hypothesis.     

CALIBRATED DIVERSITY,TREE TOPOLOGY AND THE MOTHER OF MASS EXTINCTIONS: THE LESSON OF TEMNOSPONDYLS

Abstract: Three family‐level cladistic analyses of temnospondyl amphibians are used to evaluate the impact of taxonomic rank, tree topology, and sample size on diversity profiles, origination and extinction rates, and faunal turnover. Temnospondyls are used as a case study for investigating replacement of families across the Permo‐Triassic boundary and modality of recovery in the aftermath of the end‐Permian mass extinction. Both observed and inferred (i.e. tree topology‐dependent) values of family diversity have a negligible effect on the shape of the diversity curve. However, inferred values produce both a flattening of the curve throughout the Cisuralian and a less pronounced increase in family diversity from Tatarian through to Induan than do observed values. Diversity curves based upon counts of genera and species display a clearer distinction between peaks and troughs. We use rarefaction techniques (specifically, rarefaction of the number of genera and species within families) to evaluate the effect of sampling size on the curve of estimated family‐level diversity during five time bins (Carboniferous; Cisuralian; Guadalupian–Lopingian; Early Triassic; Middle Triassic–Cretaceous). After applying rarefaction, we note that Cisuralian and Early Triassic diversity values are closer to one another than they are when the observed number of families is used; both values are also slightly higher than the Carboniferous estimated diversity. The Guadalupian–Lopingian value is lower than raw data indicate, reflecting in part the depauperate land vertebrate diversity from the late Cisuralian to the middle Guadalupian (Olson’s gap). The time‐calibrated origination and extinction rate trajectories plot out close to one another and show a peak in the Induan, regardless of the tree used to construct them. Origination and extinction trajectories are disjunct in at least some Palaeozoic intervals, and background extinctions exert a significant role in shaping temnospondyl diversity in the lowermost Triassic. Finally, species‐, genus‐, and family trajectories consistently reveal a rapid increase in temnospondyl diversity from latest Permian to earliest Triassic as well as a decline near the end of the Cisuralian. However, during the rest of the Cisuralian family diversity increases slightly and there is no evidence for a steady decline, contrary to previous reports.     

Diversity, endemism, and age distributions in macroevolutionary sources and sinks

Quantitative tests of historical hypotheses are necessary to advance our understanding of biogeographic patterns of species distributions, but direct tests are often hampered by incomplete fossil or historical records. Here we present an alternative approach in which we develop a dynamic model that allows us to test hypotheses about regional rates of taxon origination, extinction, and dispersal using information on ages and current distributions of taxa. With this model, we test two assumptions traditionally made in the context of identifying regions as "centers of origin"--that regions with high origination rates will have high diversity and high endemism. We find that these assumptions are not necessarily valid. We also develop expressions for the regional age distributions of extant taxa and show that these may yield better insight into regional evolutionary rates. We then apply our model to data on the biogeography and ages of extant genera of marine bivalves and conclude that diversity in polar regions predominantly reflects dispersal of taxa that evolved elsewhere rather than in situ origination-extinction dynamics.     

Diversity and extinction in the Cenozoic history of Caribbean reefs

Occurrences of reef corals are examined at Caribbean fossil localities to determine how biodiversity has changed within the region over the past 50 million years. Analyses of 294 species (66 genera) at 58 fossil localities show that Caribbean generic diversity rose to 44 between 50–22 Ma, ranged from 32–39 between 22–2 Ma, and dropped to 25 afterwards. Regional species diversity was high at 40–36 Ma, 28–22 Ma, and 5–2 Ma. Origination rates were elevated throughout each high diversity interval, but extinction was concentrated near the end of each interval. Regional highs of origination and extinction, therefore, differed in timing and duration, causing the observed regional diversity increases during the three remarkably long intervals of turnover. Highs of generic origination decreased in magnitude as immigration from the Mediterranean ceased, but speciation highs increased in association with emergence of the Central American isthmus. Peaks of extinction coincided with regional changes in climate and oceanic circulation. Maximum species diversities within assemblages increased to 40–60 between 50–36 Ma, and have remained relatively constant ever since. Assemblage compositions differed among localities having similar ages and environments, suggesting that the timing and pattern of turnover varied across the region. Stable diversities but variable compositions within assemblages suggest that dispersal and recruitment influenced the pattern of faunal change during turnover. Accepted: 22 August 1999     

Investigating age‐dependency of species extinction rates using dynamic survivorship analysis

Survivorship curves with taxon lifespans normalised to variations in the real‐time extinction rate (the ‘Corrected Survivorship Score’ technique) are plotted for various fossil groups. Of five groups tested at the ‘species level’ (strictly speaking, Linnean morphospecies), only the calcareous nannoplankton are found to have had a constant extinction probability with respect to morphospecies age. The planktonic foraminifer, trilobite, conodont and graptolite data all show a significant age‐dependent effect (convexity of survivorship curves), which reveals in each case a progressively increasing extinction probability as morphospecies became older. This effect is found to be much reduced for trilobite genera and absent for ammonoid families, suggesting that age‐dependency of extinction probability is primarily a characteristic of the species level in some, but not all groups. However, the pattern may be partly an artefact of taxonomic methodology. Morphospecies range data, which are gathered primarily for biostratigraphic purposes, are far from ideal for the purpose of survivorship analysis. Therefore, survivorship curves for a specially‐developed lineage phylogeny of Palaeogene planktonic foraminifera are also presented. These do not indicate a similar age‐dependency to the extinction probability with respect to either the terminal or non‐terminal lineages.