Evolutionary and biogeographical shifts in response to the Late Ordovician mass extinction

The Late Ordovician mass extinction was an interval of high extinction with inferred low ecological selectivity, resulting in little change in community structure after the event. In contrast, the mass extinction may have fundamentally changed evolutionary dynamics in the surviving groups. We investigated the phylogenetic relationships among strophomenoid brachiopods, a diverse brachiopod superfamily that was a primary component of Ordovician ecosystems. Four Ordovician families/subfamilies sampled in the analysis (Rafinesquinidae, Strophomeninae, Glyptomenidae and Furcitellinae) were reconstructed as monophyletic groups, and the base of the strophomenoid clade that dominated the Silurian recovery was reconstructed as diversifying alongside these families during the Middle Ordovician. We time‐calibrated the phylogeny and used geographical occurrences to investigate biogeographical changes in the strophomenoids through time with the R package BiogeoBEARS . Our results indicate that extinction was higher in taxa whose ranges were constrained to tropical or subtropical regions. Furthermore, our results suggest important shifts in the diversification patterns of these brachiopods after the mass extinction. While most of the strophomenoid families survived the Late Ordovician event, ecologically abundant taxonomic groups during the Ordovician were either driven to extinction, reduced in diversity, or slowly died off during the Silurian. The new abundant strophomenoid taxa derived from one clade (consisting of Silurian–Devonian groups such as Douvillinidae, Strophodontidae and Amphistrophiidae) that diversified during the post‐extinction radiation. Our results suggest the selective diversification during the Silurian radiation, rather than selective extinction in the Late Ordovician, had a greater impact on the evolutionary history of strophomenoid brachiopods.     

Geographical distribution and extinction risk: lessons from Triassic–Jurassic marine benthic organisms

Aim To evaluate the influence of geographical distribution on the extinction risk of benthic marine invertebrates using data from the fossil record, both during times of background extinction and across a mass‐extinction episode. Total geographical range is contrasted with proxies of global abundance to assess the relationships between the two essential components of geographical distribution and extinction risk. Location A global occurrence data base of fossil benthic macro‐organisms from the Triassic and Jurassic periods was used for this study. Methods Geographical distributions and biodiversity dynamics were assessed for each genus (all taxa) or species (bivalves) based on a sample‐standardized data set and palaeogeographical reconstructions. Geographical ranges were measured by the maximum great circle distance of a taxon within a stratigraphic interval. Global abundance was assessed by the number of localities at which a taxon was recorded. Widespread and rare taxa were separated using median and percentile values of the frequency distributions of occurrences. Results The frequency distribution of geographical ranges is very similar to that for modern taxa. Although no significant correlation could be established between local abundance and geographical range, proxies of global abundance are strongly correlated with geographical range. Taxon longevities are correlated with both mean geographical range and mean global abundance, but range size appears to be more critical than abundance in determining extinction risk. These results are valid when geographical distribution is treated as a trait of taxa and when assessed for individual geological stages. Main conclusions Geographical distribution is a key predictor of extinction risk of Triassic and Jurassic benthic marine invertebrates. An important exception is in the end‐Triassic mass extinction, which equally affected geographically restricted and widespread genera, as well as common and rare genera. This suggests that global diversity crises may curtail the role of geographical distribution in determining extinction risk.     

Big cat,small cat: reconstructing body size evolution in living and extinct Felidae

The evolution of body mass is a fundamental topic in evolutionary biology, because it is closely linked to manifold life history and ecological traits and is readily estimable for many extinct taxa. In this study, we examine patterns of body mass evolution in Felidae (Placentalia, Carnivora) to assess the effects of phylogeny, mode of evolution, and the relationship between body mass and prey choice in this charismatic mammalian clade. Our data set includes 39 extant and 26 extinct taxa, with published body mass data supplemented by estimates based on condylobasal length. These data were run through ‘SURFACE’ and ‘bayou’ to test for patterns of body mass evolution and convergence between taxa. Body masses of felids are significantly different among prey choice groupings (small, mixed and large). We find that body mass evolution in cats is strongly influenced by phylogeny, but different patterns emerged depending on inclusion of extinct taxa and assumptions about branch lengths. A single Ornstein–Uhlenbeck optimum best explains the distribution of body masses when first‐occurrence data were used for the fossil taxa. However, when mean occurrence dates or last known occurrence dates were used, two selective optima for felid body mass were recovered in most analyses: a small optimum around 5 kg and a large one around 100 kg. Across living and extinct cats, we infer repeated evolutionary convergences towards both of these optima, but, likely due to biased extinction of large taxa, our results shift to supporting a Brownian motion model when only extant taxa are included in analyses.     

Extinction, ecological opportunity, and the origins of global snake diversity

Snake diversity varies by at least two orders of magnitude among extant lineages, with numerous groups containing only one or two species, and several young clades exhibiting exceptional richness (>700 taxa). With a phylogeny containing all known families and subfamilies, we find that these patterns cannot be explained by background rates of speciation and extinction. The majority of diversity appears to derive from a radiation within the superfamily Colubroidea, potentially stemming from the colonization of new areas and the evolution of advanced venom-delivery systems. In contrast, negative relationships between clade age, clade size, and diversification rate suggest the potential for possible bias in estimated diversification rates, interpreted by some recent authors as support for ecologically mediated limits on diversity. However, evidence from the fossil record indicates that numerous lineages were far more diverse in the past, and that extinction has had an important impact on extant diversity patterns. Thus, failure to adequately account for extinction appears to prevent both rate- and diversity-limited models from fully characterizing richness dynamics in snakes. We suggest that clade-level extinction may provide a key mechanism for explaining negative or hump-shaped relationships between clade age and diversity, and the prevalence of ancient, species-poor lineages in numerous groups.     

Simulating the extinction of parental lineages from introgressive hybridization: the effects of fitness,initial proportions of parental taxa,and mate choice

Genomic introgression among divergent taxa following human-mediated secondary contact is a growing concern for the management and conservation of aquatic biodiversity. We simulated the composition of taxa following admixture and hybridization by independently altering three variables: (1) initial proportion of parental taxa following secondary contact; (2) fitness gradients among parental and introgressant taxa; and, (3) strength of assortative mating among these taxa. Ultimately, we established that parental taxa will trend toward extinction as introgression proceeds in spite of even a heavy fitness penalty for the hybrids. Also, the number of generations required (rate) to reach an arbitrarily determined threshold of extinction (< 5.0%) was inversely related to the strength of the relative fitness gradients among parental and derivative hybridized lineages. Moreover, the rates of extinction for parental taxa depended on the initial relative proportions in the admixture with rare taxa going extinct more rapidly than abundant taxa. Finally, the strength of assortative mating (as an evolved or reinforced mechanism of pre-mating isolation) will affect the rate of extinction. Introgressive hybridization, therefore, emerges as an important risk to structural biodiversity wherever divergent, yet reproductively compatible, taxa come together naturally or are brought together through human activities.     

Ecological limits and diversification rate: alternative paradigms to explain the variation in species richness among clades and regions

Diversification rate is one of the most important metrics in macroecological and macroevolutionary studies. Here I demonstrate that diversification analyses can be misleading when researchers assume that diversity increases unbounded through time, as is typical in molecular phylogenetic studies. If clade diversity is regulated by ecological factors, then species richness may be independent of clade age and it may not be possible to infer the rate at which diversity arose. This has substantial consequences for the interpretation of many studies that have contrasted rates of diversification among clades and regions. Often, it is possible to estimate the total diversification experienced by a clade but not diversification rate itself. I show that the evidence for ecological limits on diversity in higher taxa is widespread. Finally, I explore the implications of ecological limits for a variety of ecological and evolutionary questions that involve inferences about speciation and extinction rates from phylogenetic data.     

Marine extinction risk shaped by trait–environment interactions over 500 million years

Perhaps the most pressing issue in predicting biotic responses to present and future global change is understanding how environmental factors shape the relationship between ecological traits and extinction risk. The fossil record provides millions of years of insight into how extinction selectivity (i.e., differential extinction risk) is shaped by interactions between ecological traits and environmental conditions. Numerous paleontological studies have examined trait‐based extinction selectivity; however, the extent to which these patterns are shaped by environmental conditions is poorly understood due to a lack of quantitative synthesis across studies. We conducted a meta‐analysis of published studies on fossil marine bivalves and gastropods that span 458 million years to uncover how global environmental and geochemical changes covary with trait‐based extinction selectivity. We focused on geographic range size and life habit (i.e., infaunal vs. epifaunal), two of the most important and commonly examined predictors of extinction selectivity. We used geochemical proxies related to global climate, as well as indicators of ocean acidification, to infer average global environmental conditions. Life‐habit selectivity is weakly dependent on environmental conditions, with infaunal species relatively buffered from extinction during warmer climate states. In contrast, the odds of taxa with broad geographic ranges surviving an extinction (>2500 km for genera, >500 km for species) are on average three times greater than narrow‐ranging taxa (estimate of odds ratio: 2.8, 95% confidence interval = 2.3–3.5), regardless of the prevailing global environmental conditions. The environmental independence of geographic range size extinction selectivity emphasizes the critical role of geographic range size in setting conservation priorities.     

DNA from a 100-year-old holotype confirms the validity of a potentially extinct hummingbird species

We used mtDNA sequence data to confirm that the controversial 100-year-old holotype of the Bogotá sunangel (Heliangelus zusii) represents a valid species. We demonstrate that H. zusii is genetically well differentiated from taxa previously hypothesized to have given rise to the specimen via hybridization. Phylogenetic analyses place H. zusii as sister to a clade of mid- to high-elevation Andean species currently placed in the genera Taphrolesbia and Aglaiocercus. Heliangelus zusii, presumed extinct, has never been observed in nature by biologists. We infer that the species occupied a restricted distribution between the upper tropical and temperate zones of the northern Andes and that it was most probably driven to extinction by deforestation that accompanied human population growth during the nineteenth and early twentieth centuries. We demonstrate the feasibility of obtaining DNA from nearly microscopic tissue samples from old hummingbird specimens and suggest that these methods could be used to resolve the taxonomy of dozens of avian taxa known only from type specimens.     

Taxonomic differentiation in species richness gradients among European butterflies (Papilionoidea, Hesperioidea): contribution of macroevolutionary dynamics

We examine spatial differences in patterns of species nchness among butterfly families in Europe and North Africa When compared to global proportions for the whole region there is a surplus of Nymphalidae in northern Europe, of Piendae in North Africa and the Mediterranean islands, of Lycaenidae in Iberia and Greece, of Hesperudae in the Algarve, and a deficit of Satyridae outside the mountain areas For the Lycaenidae and Satyridae the spatial bias in numbers of species corresponds with a bias for endemism in southem Europe, regions of refuge and persistence during Pleistocene polyglaciation We argue that regional surpluses of species in at least these two families are governed more by net species production than by species maintenance Differences in species richness between families are related to ecological amplitude and dispersal capacity which determine balances between migration, clade isolation, speciation and extinction Taxa capable of migrating long distances (e g many Nymphalidae) are able to colonize distant locations but are less amenable to clade isolation, speciation or extinction, whereas, specialized taxa with limned capacity for migration (e g most Satyridae) cannot colonize distant habitats but more readily undergo clade furcation, speciation or extinction Yet, only taxa initially able to disperse and extend their ranges can undergo clade furcation Dispersal capacity divides into extnnsic and intrinsic parameters Both are influenced by environmental changes, particularly resource geography, associated with Pleistocene glacial cycles Changes in resource geography, by influencing extrinsic components of dispersal and in turn reinforcing lntrinsic components of dispersal, result in a polanzation in evolutionary dynamics, one extreme is extensive migration, gene flow and gene pool homogeneity, the other is isolation, speciation or extinction At the isolation end of this scale, the balance between clade evolution and extinction depends on the nature of environmental change and landscape structure     

Evolutionary diversification of clades of squamate reptiles

We analysed the diversification of squamate reptiles (7488 species) based on a new molecular phylogeny, and compared the results to similar estimates for passerine birds (5712 species). The number of species in each of 36 squamate lineages showed no evidence of phylogenetic conservatism. Compared with a random speciation-extinction process with parameters estimated from the size distribution of clades, the alethinophidian snakes (2600 species) were larger than expected and 13 clades, each having fewer than 20 species, were smaller than expected, indicating rate heterogeneity. From a lineage-through-time plot, we estimated that a provisional rate of lineage extinction (0.66 per Myr) was 94% of the rate of lineage splitting (0.70 per Myr). Diversification in squamate lineages was independent of their stem age, but strongly related to the area of the region within which they occur. Tropical vs. temperate latitude exerted a marginally significant influence on species richness. In comparison with passerine birds, squamates share several clade features, including: (1) independence of species richness and age; (2) lack of phylogenetic signal with respect to clade size; (3) general absence of exceptionally large clades; (4) over-representation of small clades; (5) influence of region size on clade size; and (6) similar rates of speciation and extinction. The evidence for both groups suggests that clade size has achieved long-term equilibrium, suggesting negative feedback of species richness on the rate of diversification.     

Hosts of the Plio-Pleistocene past reflect modern-day coral vulnerability

The risk of global extinction of reef-building coral species is increasing. We evaluated extinction risk using a biological trait-based resiliency index that was compared with Caribbean extinction during the Plio-Pleistocene, and with extinction risk determined by the International Union for Conservation of Nature (IUCN). Through the Plio-Pleistocene, the Caribbean supported more diverse coral assemblages than today and shared considerable overlap with contemporary Indo-Pacific reefs. A clear association was found between extant Plio-Pleistocene coral genera and our positive resilience scores. Regional extinction in the past and vulnerability in the present suggests that Pocillopora, Stylophora and foliose Pavona are among the most susceptible taxa to local and regional isolation. These same taxa were among the most abundant corals in the Caribbean Pliocene. Therefore, a widespread distribution did not equate with immunity to regional extinction. The strong relationship between past and present vulnerability suggests that regional extinction events are trait-based and not merely random episodes. We found several inconsistencies between our data and the IUCN scores, which suggest a need to critically re-examine what constitutes coral vulnerability.     

Biological hierarchies and the nature of extinction

Hierarchy theory recognises that ecological and evolutionary units occur in a nested and interconnected hierarchical system, with cascading effects occurring between hierarchical levels. Different biological disciplines have routinely come into conflict over the primacy of different forcing mechanisms behind evolutionary and ecological change. These disconnects arise partly from differences in perspective (with some researchers favouring ecological forcing mechanisms while others favour developmental/historical mechanisms), as well as differences in the temporal framework in which workers operate. In particular, long‐term palaeontological data often show that large‐scale (macro) patterns of evolution are predominantly dictated by shifts in the abiotic environment, while short‐term (micro) modern biological studies stress the importance of biotic interactions. We propose that thinking about ecological and evolutionary interactions in a hierarchical framework is a fruitful way to resolve these conflicts. Hierarchy theory suggests that changes occurring at lower hierarchical levels can have unexpected, complex effects at higher scales due to emergent interactions between simple systems. In this way, patterns occurring on short‐ and long‐term time scales are equally valid, as changes that are driven from lower levels will manifest in different forms at higher levels. We propose that the dual hierarchy framework fits well with our current understanding of evolutionary and ecological theory. Furthermore, we describe how this framework can be used to understand major extinction events better. Multi‐generational attritional loss of reproductive fitness (MALF) has recently been proposed as the primary mechanism behind extinction events, whereby extinction is explainable solely through processes that result in extirpation of populations through a shutdown of reproduction. While not necessarily explicit, the push to explain extinction through solely population‐level dynamics could be used to suggest that environmentally mediated patterns of extinction or slowed speciation across geological time are largely artefacts of poor preservation or a coarse temporal scale. We demonstrate how MALF fits into a hierarchical framework, showing that MALF can be a primary forcing mechanism at lower scales that still results in differential survivorship patterns at the species and clade level which vary depending upon the initial environmental forcing mechanism. Thus, even if MALF is the primary mechanism of extinction across all mass extinction events, the primary environmental cause of these events will still affect the system and result in differential responses. Therefore, patterns at both temporal scales are relevant.     

Decoupling of morphological disparity and taxic diversity during the adaptive radiation of anomodont therapsids

Adaptive radiations are central to macroevolutionary theory. Whether triggered by acquisition of new traits or ecological opportunities arising from mass extinctions, it is debated whether adaptive radiations are marked by initial expansion of taxic diversity or of morphological disparity (the range of anatomical form). If a group rediversifies following a mass extinction, it is said to have passed through a macroevolutionary bottleneck, and the loss of taxic or phylogenetic diversity may limit the amount of morphological novelty that it can subsequently generate. Anomodont therapsids, a diverse clade of Permian and Triassic herbivorous tetrapods, passed through a bottleneck during the end-Permian mass extinction. Their taxic diversity increased during the Permian, declined significantly at the Permo–Triassic boundary and rebounded during the Middle Triassic before the clade''s final extinction at the end of the Triassic. By sharp contrast, disparity declined steadily during most of anomodont history. Our results highlight three main aspects of adaptive radiations: (i) diversity and disparity are generally decoupled; (ii) models of radiations following mass extinctions may differ from those triggered by other causes (e.g. trait acquisition); and (iii) the bottleneck caused by a mass extinction means that a clade can emerge lacking its original potential for generating morphological variety.     

Effects of habitat size and isolation on species immigration–extinction dynamics and community nestedness in a desert river system

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THE EARLY DIVERSIFICATION HISTORY OF DIDELPHID MARSUPIALS: A WINDOW INTO SOUTH AMERICA'S “SPLENDID ISOLATION”

The geological record of South American mammals is spatially biased because productive fossil sites are concentrated at high latitudes. As a result, the history of mammalian diversification in Amazonia and other tropical biomes is largely unknown. Here we report diversification analyses based on a time‐calibrated molecular phylogeny of opossums (Didelphidae), a species‐rich clade of mostly tropical marsupials descended from a Late Oligocene common ancestor. Optimizations of habitat and geography on this phylogeny suggest that (1) basal didelphid lineages inhabited South American moist forests; (2) didelphids did not diversify in dry‐forest habitats until the Late Miocene; and (3) most didelphid lineages did not enter North America until the Pliocene. We also summarize evidence for an Early‐ to Middle‐Miocene mass extinction event, for which alternative causal explanations are discussed. To the best of our knowledge, this study provides the first published molecular‐phylogenetic evidence for mass extinction in any animal clade, and it is the first time that evidence for such an event (in any plant or animal taxon) has been tested for statistical significance. Potentially falsifying observations that could help discriminate between the proposed alternative explanations for didelphid mass extinction may be obtainable from diversification analyses of other sympatric mammalian groups.     

A phylogeny of the fossil and extant zeiform-like fishes, Upper Cretaceous to Recent, with comments on the putative zeomorph clade (Acanthomorpha)

Tyler, J. C. & Santini, F. (2005). A phylogeny of the fossil and extant zeiform-like fishes, Upper Cretaceous to Recent, with comments on the putative zeomorph clade (Acanthomorpha). — Zoological Scripta , ** , ***–***.
A phylogenetic hypothesis based on 107 morphological characters is proposed for a data set of 43 taxa. Thirty-three are extant and belong to the orders Zeiformes (20 taxa), Caproiformes (2), Tetraodontiformes (2), Beryciformes (3), Stephanoberyciformes (3) and Perciformes (3). Ten are fossil taxa previously assigned to the Zeiformes (3), Caproiformes (1), Tetraodontiformes (2), Perciformes (1), and to two extinct Eocene families, the Sorbinipercidae (2) and the Zorzinichthyidae (1). This analysis indicates the existence of a previously undocumented clade formed by the families Sorbinipercidae + Zorzinichthyidae that may be related to the tetraodontiforms. It also shows that two uppermost Palaeocene species, Archaeozeus skamolensis and Protozeus kuehnei , sequentially represent the two most basal lineages of zeiforms, whereas the most ancient known zeiform, the Upper Cretaceous Cretazeus rinaldii , belongs within the clade of extant species in a polytomy with many other zeiform lineages. A reduced data set of 25 mostly zeiform taxa, after the removal of most outgroups, shows at least weak support for Cretazeus being nested deeply within the extant zeiforms; such a placement would indicate that at least six lineages of zeiforms were present during the Upper Cretaceous, and survived the Cretaceous/Tertiary (K/T) extinction to radiate in Cenozoic seas.     

Revisiting the impacts of non-random extinction on the tree-of-life

The tree-of-life represents the diversity of living organisms. Species extinction and the concomitant loss of branches from the tree-of-life is therefore a major conservation concern. There is increasing evidence indicating that extinction is phylogenetically non-random, such that if one species is vulnerable to extinction so too are its close relatives. However, the impact of non-random extinctions on the tree-of-life has been a matter of recent debate. Here, we combine simulations with empirical data on extinction risk in mammals. We demonstrate that phylogenetically clustered extinction leads to a disproportionate loss of branches from the tree-of-life, but that the loss of their summed lengths is indistinguishable from random extinction. We argue that under a speciational model of evolution, the number of branches lost might be of equal or greater consequences than the loss of summed branch lengths. We therefore suggest that the impact of non-random extinction on the tree-of-life may have been underestimated.     

Body length of bony fishes was not a selective factor during the biggest mass extinction of all time

The Permo‐Triassic mass extinction devastated life on land and in the sea, but it is not clear why some species survived and others went extinct. One explanation is that lineage loss during mass extinctions is a random process in which luck determines which species survive. Alternatively, a phylogenetic signal in extinction may indicate a selection process operating on phenotypic traits. Large body size has often emerged as an extinction risk factor in studies of modern extinction risk, but this is not so commonly the case for mass extinctions in deep time. Here, we explore the evolution of non‐teleostean Actinopterygii (bony fishes) from the Devonian to the present day, and we concentrate on the Permo‐Triassic mass extinction. We apply a variety of time‐scaling metrics to date the phylogeny, and show that diversity peaked in the latest Permian and declined severely during the Early Triassic. In line with previous evidence, we find the phylogenetic signal of extinction increases across the mass extinction boundary: extinction of species in the earliest Triassic is more clustered across phylogeny compared to the more randomly distributed extinction signal in the late Permian. However, body length plays no role in differential survival or extinction of taxa across the boundary. In the case of fishes, size did not determine which species survived and which went extinct, but phylogenetic signal indicates that the mass extinction was not a random field of bullets.     

Phylogenetic relationships within a patagonian clade of reptiles (Liolaemidae: Phymaturus) based on DNA sequences and morphology

Phymaturus is a clade of lizards that occurs at moderate to high elevations in western Argentina and the adjacent central region of Chile, as well as in various volcanic plateaus of the Patagonian region of Argentina. This genus had previously been divided into two groups: the patagonicus and the palluma groups. In this study, we analyzed relationships within the patagonicus group. The data set was built for 23 species plus nine other terminal taxa of undetermined taxonomic status. In total, 10,631 bp (ND4, Cytb, 12S, COI, five protein coding nuclear genes and seven anonymous nuclear loci) and 254 morphological characters were analyzed in a combined data set for 35 ingroup taxa and nine outgroups. We also ran separate DNA sequence and morphological data sets. We identified four main clades, and revealed congruencies and incongruences with previous studies. The indistinctus clade is recovered as the most basal within the patagonicus group in the strict parsimony analysis, while the somuncurensis clade is the most basal under Bayesian inference. The previously recovered calcogaster clade resulted paraphyletic in both analyses and part of their species are included in a redefined somuncurensis clade. We found low support at basal nodes provoked in part by contradictory evidence shown by rogue taxa. We show the phylogenetic information given by each partition/marker and how they contribute to relationships found in the total evidence analysis. We discuss the phylogenetic position of Phymaturus manuelae, Phymaturus tenebrosus, and Phymaturus patagonicus.