Testing for a decline in diversity prior to extinction: Languedocian (latest mid‐Cambrian) distribution of cinctans (Echinodermata) in the Iberian Chains,NE Spain

Abstract: The middle Cambrian strata of the Iberian Chains (north‐eastern Spain) and the Montagne Noire (southern France) record an adaptative radiation of cinctans and trilobites, which spanned the Leonian–early Languedocian interval. A diachronous diversity peak was reached by both benthic groups when favourable palaeoenvironmental conditions (clayey vs. silty substrates) were established. The acme in diversity was followed by a gradual decline and a barren interval associated with the onset of the mid‐Languedocian regression, well constrained throughout the western Mediterranean region. For trilobites, the aftermath of the regression is characterized by a late‐Languedocian major faunal turnover of families, followed by a renewed Furongian–early Tremadocian radiation related to the stepwise immigration of trilobite invaders from northern and eastern Gondwana, under persistent transgressive conditions. In contrast, the cinctans reappeared only patchily in late‐Languedocian monospecific coquinas and finally disappeared before the Furongian. Thus, the late Languedocian is a crucial interval in which to analyse the decline in diversity and final extinction of cinctans in the aftermath of the mid‐Languedocian regression.     

Song evolution,speciation, and vocal learning in passerine birds

Phenotypic divergence can promote reproductive isolation and speciation, suggesting a possible link between rates of phenotypic evolution and the tempo of speciation at multiple evolutionary scales. To date, most macroevolutionary studies of diversification have focused on morphological traits, whereas behavioral traits─including vocal signals─are rarely considered. Thus, although behavioral traits often mediate mate choice and gene flow, we have a limited understanding of how behavioral evolution contributes to diversification. Furthermore, the developmental mode by which behavioral traits are acquired may affect rates of behavioral evolution, although this hypothesis is seldom tested in a phylogenetic framework. Here, we examine evidence for rate shifts in vocal evolution and speciation across two major radiations of codistributed passerines: one oscine clade with learned songs (Thraupidae) and one suboscine clade with innate songs (Furnariidae). We find that evolutionary bursts in rates of speciation and song evolution are coincident in both thraupids and furnariids. Further, overall rates of vocal evolution are higher among taxa with learned rather than innate songs. Taken together, these findings suggest an association between macroevolutionary bursts in speciation and vocal evolution, and that the tempo of behavioral evolution can be influenced by variation in developmental modes among lineages.     

Late Miocene diversification of the genus Hydrochus (Coleoptera, Hydrochidae) in the west Mediterranean area

We provide a reconstruction of the phylogenetic relationships, the geographical and temporal origin, and the mode of diversification of the Mediterranean species of the aquatic beetle family Hydrochidae (Coleoptera, Hydrophiloidea). A total of ca. 3KB of sequence data of three mitochondrial and two nuclear genes were used to reconstruct the phylogeny of 62 specimens of 21 species of Hydrochus, including all western Mediterranean species but one. We estimated the times of divergence using Bayesian methods and an evolutionary rate of 0.0115 substitutions/site/MY, and used an ultrametric calibrated tree to construct a Lineage Through Time (LTT) plot to test alternative models of diversification. A well resolved, well supported phylogeny showed that all western Mediterranean Hydrochus formed a clade, sister to a group including species with a central and eastern European distribution. The origin of the western Mediterranean clade was estimated to be at ca. 13MY, and the speciation events took place between this time and the end of the Messinian, at about 5.3MY. The LTT plot best fitted a model with a shift in the rate of diversification at ca. 8 MY, with a single speciation event (originating two Iberian endemics) subsequent to this period. We conclude that most of the western Mediterranean species of Hydrochidae, including the Ibero-Maghrebian endemics, are ancient elements likely to have remained in the same geographical area since their Miocene origin. Our results add to a growing body of evidence showing the importance of Mediterranean long-term, Tertiary refugia as both cradles and museums of diversity.     

Mediterranean diversification of the grass-feeding Anisopliina beetles (Scarabaeidae, Rutelinae, Anomalini) as inferred by bootstrap-averaged dispersal–vicariance analysis

Aim The circum‐Mediterranean region is one of the most complex regions of the Earth in terms of geography and natural history. The Old World species of the beetle subtribe Anisopliina (Scarabaeidae) feed almost exclusively on the pollen of grasses (Poaceae). Within this group, the ‘anisopliine clade’ forms a monophyletic group distributed mainly in the circum‐Mediterranean region. Here, we reconstruct the biogeographical history of the anisopliine beetles in relation to the diversification of grasses, and compare this reconstruction with previous hypotheses concerning the evolution of the Mediterranean fauna and with palaeogeographical accounts of the history of this region. Location The Mediterranean region, including North Africa, the Western Mediterranean, Balkans–Anatolia, Middle East and Caucasus. Methods Dispersal–vicariance analysis (diva ) was used to reconstruct ancestral distributions based on the morphological phylogeny and to infer the biogeographical processes that have shaped the observed distribution patterns. To account for phylogenetic uncertainty in the biogeographical reconstruction, we ran alternative ancestral distributions derived by diva over a sample of trees obtained by bootstrapping the original data set, reflecting the relative confidence of the ancestral areas on the various clades in the phylogeny. Results The Eastern Mediterranean region and the Caucasus are inferred as the ancestral area of most of the anisopliine lineages. The Eastern Mediterranean region is also reconstructed as the source area of the majority of dispersal events, in particular towards North Africa and the Western Mediterranean. The Iberian Peninsula is inferred as part of the ancestral distribution of the anisopliine clade but also as the setting of several independent colonization events via both the North African platform (Anthoplia) and a European dispersal route (Anisoplia). Main conclusions Our results confirm the role played by the Eastern Mediterranean as an evolutionary cradle of diversity for Mediterranean lineages. This can be explained by a recent and intense orogenic activity that might have promoted isolation and allopatric speciation within lineages. Both the Anomalini fossil record and the close association of anisopliine beetles with grasses suggest that the anisopliine clade originated in the Late Tertiary and that its spatial and temporal evolution within the Mediterranean Basin coincided with that of its major food source, the Mediterranean Poaceae.     

Evolution and biogeography of the endemic Roucela complex (Campanulaceae: Campanula) in the Eastern Mediterranean

At the intersection of geological activity, climatic fluctuations, and human pressure, the Mediterranean Basin – a hotspot of biodiversity – provides an ideal setting for studying endemism, evolution, and biogeography. Here, we focus on the Roucela complex (Campanula subgenus Roucela), a group of 13 bellflower species found primarily in the eastern Mediterranean Basin. Plastid and low‐copy nuclear markers were employed to reconstruct evolutionary relationships and estimate divergence times within the Roucela complex using both concatenation and species tree analyses. Niche modeling, ancestral range estimation, and diversification analyses were conducted to provide further insights into patterns of endemism and diversification through time. Diversification of the Roucela clade appears to have been primarily the result of vicariance driven by the breakup of an ancient landmass. We found geologic events such as the formation of the mid‐Aegean trench and the Messinian Salinity Crisis to be historically important in the evolutionary history of this group. Contrary to numerous past studies, the onset of the Mediterranean climate has not promoted diversification in the Roucela complex and, in fact, may be negatively affecting these species. This study highlights the diversity and complexity of historical processes driving plant evolution in the Mediterranean Basin.     

Corolla morphology influences diversification rates in bifid toadflaxes (Linaria sect. Versicolores)

Background and Aims

The role of flower specialization in plant speciation and evolution remains controversial. In this study the evolution of flower traits restricting access to pollinators was analysed in the bifid toadflaxes (Linaria sect. Versicolores), a monophyletic group of ∼30 species and subspecies with highly specialized corollas.

Methods

A time-calibrated phylogeny based on both nuclear and plastid DNA sequences was obtained using a coalescent-based method, and flower morphology was characterized by means of morphometric analyses. Directional trends in flower shape evolution and trait-dependent diversification rates were jointly analysed using recently developed methods, and morphological shifts were reconstructed along the phylogeny. Pollinator surveys were conducted for a representative sample of species.

Key Results

A restrictive character state (narrow corolla tube) was reconstructed in the most recent common ancestor of Linaria sect. Versicolores. After its early loss in the most species-rich clade, this character state has been convergently reacquired in multiple lineages of this clade in recent times, yet it seems to have exerted a negative influence on diversification rates. Comparative analyses and pollinator surveys suggest that the narrow- and broad-tubed flowers are evolutionary optima representing divergent strategies of pollen placement on nectar-feeding insects.

Conclusions

The results confirm that different forms of floral specialization can lead to dissimilar evolutionary success in terms of diversification. It is additionally suggested that opposing individual-level and species-level selection pressures may have driven the evolution of pollinator-restrictive traits in bifid toadflaxes.     

The correlated evolution of three-dimensional reproductive structures between male and female damselflies

For many taxa, species are defined by the morphologies of reproductive structures. In many odonates, these structures are the cerci of males (used to hold females during mating) and the thoracic plates of females where the male cerci contact the females' bodies. A previous study showed that the shapes of cerci of Enallagma males (Zygoptera: Coenagrionidae) are best explained by an evolutionary model of punctuated change at the time of speciation, with a homogeneous rate of change across the entire phylogeny of the genus. In the present study, we examine the evolution of shape change in the corresponding female plates. We found that, like male cerci, the shapes of Enallagma female thoracic plates could best be explained by an evolutionary model of punctuated change at the time of speciation, with a homogeneous rate of change across the clade. Moreover, the evolutionary contrasts quantifying the rates of change in male cerci and female thoracic plates were positively related across the history of the clade, demonstrating that these male and female structures evolve in a correlated fashion. This pattern of evolution suggests that these structures are primary signals of species identity during mating.     

Large-scale patterns of diversification in the widespread legume genus Senna and the evolutionary role of extrafloral nectaries

Unraveling the diversification history of old, species-rich and widespread clades is difficult because of extinction, undersampling, and taxonomic uncertainty. In the context of these challenges, we investigated the timing and mode of lineage diversification in Senna (Leguminosae) to gain insights into the evolutionary role of extrafloral nectaries (EFNs). EFNs secrete nectar, attracting ants and forming ecologically important ant-plant mutualisms. In Senna, EFNs characterize one large clade (EFN clade), including 80% of its 350 species. Taxonomic accounts make Senna the largest caesalpinioid genus, but quantitative comparisons to other taxa require inferences about rates. Molecular dating analyses suggest that Senna originated in the early Eocene, and its major lineages appeared during early/mid Eocene to early Oligocene. EFNs evolved in the late Eocene, after the main radiation of ants. The EFN clade diversified faster, becoming significantly more species-rich than non-EFN clades. The shift in diversification rates associated with EFN evolution supports the hypothesis that EFNs represent a (relatively old) key innovation in Senna. EFNs may have promoted the colonization of new habitats appearing with the early uplift of the Andes. This would explain the distinctive geographic concentration of the EFN clade in South America.     

How traits shape trees: new approaches for detecting character state‐dependent lineage diversification

Biologists have long sought to understand the processes underlying disparities in clade size across the tree of life and the extent to which such clade size differences can be attributed to the evolution of particular traits. The association of certain character states with species‐rich clades suggests that trait evolution can lead to increased diversification, but such a pattern could also arise due other processes, such as directional trait evolution. Recent advances in phylogenetic comparative methods have provided new statistical approaches for distinguishing between these intertwined and potentially confounded macroevolutionary processes. Here, we review the historical development of methods for detecting state‐dependent diversification and explore what new methods have revealed about classic examples of traits that affect diversification, including evolutionary dead ends, key innovations and geographic traits. Applications of these methods thus far collectively suggest that trait diversity commonly arises through the complex interplay between transition, speciation and extinction rates and that long hypothesized evolutionary dead ends and key innovations are instead often cases of directional trends in trait evolution.     

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     

The Omo-Turkana Basin fossil hominins and their contribution to our understanding of human evolution in Africa

The Omo-Turkana Basin, including the hominin fossil sites around Lake Turkana and the sites along the lower reaches of the Omo River, has made and continues to make an important contribution to improving our murky understanding of human evolution. This review highlights the various ways the Omo-Turkana Basin fossil record has contributed to, and continues to challenge, interpretations of human evolution. Despite many diagrams that look suspiciously like comprehensive hypotheses about human evolutionary history, any sensible paleoanthropologist knows that the early hominin fossil record is too meager to do anything other than offer very provisional statements about hominin taxonomy and phylogeny. If history tells us anything, it is that we still have much to learn about the hominin clade. Thus, we summarize the current state of knowledge of the hominin species represented at the Omo-Turkana Basin sites. We then focus on three specific topics for which the fossil evidence is especially relevant: the origin and nature of Paranthropus; the origin and nature of early Homo; and the ongoing debate about whether the pattern of human evolution is more consistent with speciation by cladogenesis, with greater taxonomic diversity or with speciation by anagenetic transformation, resulting in less taxonomic diversity and a more linear interpretation of human evolutionary history.     

Explaining Andean megadiversity: the evolutionary and ecological causes of glassfrog elevational richness patterns

The Tropical Andes are an important global biodiversity hotspot, harbouring extraordinarily high richness and endemism. Although elevational richness and speciation have been studied independently in some Andean groups, the evolutionary and ecological processes that explain elevational richness patterns in the Andes have not been analysed together. Herein, we elucidate the processes underlying Andean richness patterns using glassfrogs (Centrolenidae) as a model system. Glassfrogs show the widespread mid‐elevation diversity peak for both local and regional richness. Remarkably, these patterns are explained by greater time (montane museum) rather than faster speciation at mid‐elevations (montane species pump), despite the recency of the major Andean uplift. We also show for the first time that rates of climatic‐niche evolution and elevational change are related, supporting the hypothesis that climatic‐niche conservatism decelerates species' shifts in elevational distributions and underlies the mid‐elevation richness peak. These results may be relevant to other Andean clades and montane systems globally.     

Evolutionary history of the little fire ant Wasmannia auropunctata before global invasion: inferring dispersal patterns,niche requirements and past and present distribution within its native range

The evolutionary history of invasive species within their native range may involve key processes that allow them to colonize new habitats. Therefore, phylogeographic studies of invasive species within their native ranges are useful to understand invasion biology in an evolutionary context. Here we integrated classical and Bayesian phylogeographic methods using mitochondrial and nuclear DNA markers with a palaeodistribution modelling approach, to infer the phylogeographic history of the invasive ant Wasmannia auropunctata across its native distribution in South America. We discuss our results in the context of the recent establishment of this mostly tropical species in the Mediterranean region. Our Bayesian phylogeographic analysis suggests that the common ancestor of the two main clades of W. auropunctata occurred in central Brazil during the Pliocene. Clade A would have differentiated northward and clade B southward, followed by a secondary contact beginning about 380 000 years ago in central South America. There were differences in the most suitable habitats among clades when considering three distinct climatic periods, suggesting that genetic differentiation was accompanied by changes in niche requirements, clade A being a tropical lineage and clade B a subtropical and temperate lineage. Only clade B reached more southern latitudes, with a colder climate than that of northern South America. This is concordant with the adaptation of this originally tropical ant species to temperate climates prior to its successful establishment in the Mediterranean region. This study highlights the usefulness of exploring the evolutionary history of invasive species within their native ranges to better understand biological invasions.     

When is sympatric speciation truly adaptive? An analysis of the joint evolution of resource utilization and assortative mating

The plausibility of sympatric speciation has long been debated among evolutionary ecologists. The process necessarily involves two key elements: the stable coexistence of at least two ecologically distinct types and the emergence of reproductive isolation. Recent theoretical studies within the theoretical framework of adaptive dynamics have shown how both these processes can be driven by natural selection. In the standard scenario, a population first evolves to an evolutionary branching point, next, disruptive selection promotes ecological diversification within the population, and, finally, the fitness disadvantage of intermediate types induces a selection pressure for assortative mating behaviour, which leads to reproductive isolation and full speciation. However, the full speciation process has been mostly studied through computer simulations and only analysed in part. Here I present a complete analysis of the whole speciation process by allowing for the simultaneous evolution of the branching ecological trait as well as a continuous trait controlling mating behaviour. I show how the joint evolution can be understood in terms of a gradient landscape, where the plausibility of different evolutionary paths can be evaluated graphically. I find sympatric speciation unlikely for scenarios with a continuous, unimodal, distribution of resources. Rather, ecological settings where the fitness inferiority of intermediate types is preserved during the ecological branching are more likely to provide opportunity for adaptive, sympatric speciation. Such scenarios include speciation due to predator avoidance or specialization on discrete resources. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Naming diversity in an evolutionary context: Phylogenetic definitions of the Roucela clade (Campanulaceae/Campanuloideae) and the cryptic taxa within

In recent times, evolution has become a central tenet of taxonomy, but nomenclature has consistently been decoupled from the tree‐thinking process, often leading to significant issues in reconciling traditional (Linnaean) names with clades in the Tree of Life. Recent evolutionary studies on the Roucela clade, a group of endemic plants found in the Mediterranean Basin, motivated the establishment of phylogenetic concepts to formally anchor clade names on the Campanuloideae (Campanulaceae) tree. These concepts facilitate communication of clades that approximate traditionally defined groups, in addition to naming newly discovered cryptic diversity in a phylogenetic framework.     

Integrating environmental,molecular, and morphological data to unravel an ice‐age radiation of arctic‐alpine Campanula in western North America

Many arctic‐alpine plant genera have undergone speciation during the Quaternary. The bases for these radiations have been ascribed to geographic isolation, abiotic and biotic differences between populations, and/or hybridization and polyploidization. The Cordilleran Campanula L. (Campanulaceae Juss.), a monophyletic clade of mostly endemic arctic‐alpine taxa from western North America, experienced a recent and rapid radiation. We set out to unravel the factors that likely influenced speciation in this group. To do so, we integrated environmental, genetic, and morphological datasets, tested biogeographic hypotheses, and analyzed the potential consequences of the various factors on the evolutionary history of the clade. We created paleodistribution models to identify potential Pleistocene refugia for the clade and estimated niche space for individual taxa using geographic and climatic data. Using 11 nuclear loci, we reconstructed a species tree and tested biogeographic hypotheses derived from the paleodistribution models. Finally, we tested 28 morphological characters, including floral, vegetative, and seed characteristics, for their capacity to differentiate taxa. Our results show that the combined effect of Quaternary climatic variation, isolation among differing environments in the mountains in western North America, and biotic factors influencing floral morphology contributed to speciation in this group during the mid‐Pleistocene. Furthermore, our biogeographic analyses uncovered asynchronous consequences of interglacial and glacial periods for the timing of refugial isolation within the southern and northwestern mountains, respectively. These findings have broad implications for understanding the processes promoting speciation in arctic‐alpine plants and the rise of numerous endemic taxa across the region.     

Shifts in diversification rates and host jump frequencies shaped the diversity of host range among Sclerotiniaceae fungal plant pathogens

The range of hosts that a parasite can infect in nature is a trait determined by its own evolutionary history and that of its potential hosts. However, knowledge on host range diversity and evolution at the family level is often lacking. Here, we investigate host range variation and diversification trends within the Sclerotiniaceae, a family of Ascomycete fungi. Using a phylogenetic framework, we associate diversification rates, the frequency of host jump events and host range variation during the evolution of this family. Variations in diversification rate during the evolution of the Sclerotiniaceae define three major macro‐evolutionary regimes with contrasted proportions of species infecting a broad range of hosts. Host–parasite cophylogenetic analyses pointed towards parasite radiation on distant hosts long after host speciation (host jump or duplication events) as the dominant mode of association with plants in the Sclerotiniaceae. The intermediate macro‐evolutionary regime showed a low diversification rate, high frequency of duplication events and the highest proportion of broad host range species. Our findings suggest that the emergence of broad host range fungal pathogens results largely from host jumps, as previously reported for oomycete parasites, probably combined with low speciation rates. These results have important implications for our understanding of fungal parasites evolution and are of particular relevance for the durable management of disease epidemics.     

Macroevolutionary trends in the Dinosauria: Cope's rule

Cope's rule is the tendency for body size to increase over time along a lineage. A set of 65 phylogenetically independent comparisons, between earlier and later genera, show that Cope's rule applied in dinosaurs: later genera were on average about 25% longer than the related earlier genera to which they were compared. The tendency for size to increase was not restricted to a particular clade within the group, nor to a particular time within its history. Small lineages were more likely to increase in size, and large lineages more likely to decrease: this pattern may indicate an intermediate optimum body size, but can also be explained as an artefact of data error. The rate of size increase estimated from the phylogenetic comparisons is significantly higher than the rate seen across the fauna as a whole. This difference could indicate that within-lineage selection for larger size was opposed by clade selection favouring smaller size, but data limitations mean that alternative explanations (which we discuss) cannot be excluded. We discuss ways of unlocking the full potential usefulness of phylogenies for studying the dynamics of evolutionary trends.     

A phylogenetic analysis of macroevolutionary patterns in fermentative yeasts

When novel sources of ecological opportunity are available, physiological innovations can trigger adaptive radiations. This could be the case of yeasts (Saccharomycotina), in which an evolutionary novelty is represented by the capacity to exploit simple sugars from fruits (fermentation). During adaptive radiations, diversification and morphological evolution are predicted to slow‐down after early bursts of diversification. Here, we performed the first comparative phylogenetic analysis in yeasts, testing the “early burst” prediction on species diversification and also on traits of putative ecological relevance (cell‐size and fermentation versatility). We found that speciation rates are constant during the time‐range we considered (ca., 150 millions of years). Phylogenetic signal of both traits was significant (but lower for cell‐size), suggesting that lineages resemble each other in trait‐values. Disparity analysis suggested accelerated evolution (diversification in trait values above Brownian Motion expectations) in cell‐size. We also found a significant phylogenetic regression between cell‐size and fermentation versatility (R² = 0.10), which suggests correlated evolution between both traits. Overall, our results do not support the early burst prediction both in species and traits, but suggest a number of interesting evolutionary patterns, that warrant further exploration. For instance, we show that the Whole Genomic Duplication that affected a whole clade of yeasts, does not seems to have a statistically detectable phenotypic effect at our level of analysis. In this regard, further studies of fermentation under common‐garden conditions combined with comparative analyses are warranted.