Hierarchy in adaptive radiation: A case study using the Carnivora (Mammalia)

Simpson's “early burst” model of adaptive radiation was intended to explain the early proliferation of morphological and functional variation in diversifying clades. Yet, despite much empirical testing, questions remain regarding its frequency across the tree of life. Here, we evaluate the support for an early burst model of adaptive radiation in 14 ecomorphological traits plus body mass for the extant mammalian order Carnivora and its constituent families. We find strong support for early bursts of dental evolution, suggesting a classic Simpsonian adaptive radiation along dietary resource axes. However, the signal of this early burst is not consistently recovered in analyses at the family level, where support for a variety of different models emerges. Furthermore, we find no evidence for early burst–like dynamics in size–related traits, and Bayesian analyses of evolutionary correlations corroborate a decoupling of size and dental evolution, driven in part by dietary specialization. Our results are consistent with the perspective that trait diversification unfolds hierarchically, with early bursts restricted to traits associated with higher level niches, such as macrohabitat use or dietary strategy, and thus with the origins of higher taxa. The lack of support for early burst adaptive radiation in previous phylogenetic studies may be a consequence of focusing on low‐level niche traits (i.e., those associated with microhabitat use) in clades at shallow phylogenetic levels. A richer understanding of early burst adaptive radiation will require a renewed focus on functional traits and their evolution over higher level clades.     

Diversification rates have declined in the Malagasy herpetofauna

The evolutionary origins of Madagascar''s biodiversity remain mysterious despite the fact that relative to land area, there is no other place with consistently high levels of species richness and endemism across a range of taxonomic levels. Most efforts to explain diversification on the island have focused on geographical models of speciation, but recent studies have begun to address the island''s accumulation of species through time, although with conflicting results. Prevailing hypotheses for diversification on the island involve either constant diversification rates or scenarios where rates decline through time. Using relative-time-calibrated phylogenies for seven endemic vertebrate clades and a model-fitting framework, I find evidence that diversification rates have declined through time on Madagascar. I show that diversification rates have clearly declined throughout the history of each clade, and models invoking diversity-dependent reductions to diversification rates best explain the diversification histories for each clade. These results are consistent with the ecological theory of adaptive radiation, and, coupled with ancillary observations about ecomorphological and life-history evolution, strongly suggest that adaptive radiation was an important formative process for one of the most species-rich regions on the Earth. These results cast the Malagasy biota in a new light and provide macroevolutionary justification for conservation initiatives.     

Spatio‐temporal history of the endemic genera of Madagascar

Madagascar is renowned for its unparalleled species richness and levels of endemism, which have led, in combination with species extinction caused by an unprecedented rate of anthropogenic deforestation, to its designation as one of the most important biodiversity hotspots. It is home to 10 650 species (84% endemic) of angiosperms in 1621 genera (19% endemic). During the last two centuries, botanists have focused their efforts on the provision of a taxonomic framework for the flora of the island, but much remains to be investigated regarding the evolutionary processes that have shaped Madagascan botanical diversity. In this article, we review the current state of phylogenetic and biogeographical knowledge of the endemic angiosperm genera. We also propose a new stratified biogeographical model, based on palaeogeographical evidence, allowing the inference of the spatio‐temporal history of Madagascan taxa. The implications of past climate change and extinction events on the evolutionary history of the endemic genera are also discussed in depth. Phylogenetic information was available for 184 of the 310 endemic genera (59.3%) and divergence time estimates were available for 67 (21.6%). Based on this evidence, we show the importance of phylogenetic clustering in the assemblage of the current Madagascan diversity (26% of the genera have a sister lineage from Madagascar) and confirm the strong floristic affinities with Africa, South‐East Asia and India (22%, 9.1% and 6.2% of the genera, respectively). The close links with the Comoros, Mascarenes and Seychelles are also discussed. These results also support an Eocene/Oligocene onset for the origin of the Madagascan generic endemic flora, with the majority arising in the Miocene or more recently. These results therefore de‐emphasize the importance of the Gondwanan break‐up on the evolution of the flora. There is, however, some fossil evidence suggesting that recent extinctions (e.g. Sarcolaenaceae, a current Madagascan endemic, in southern Africa) might blur vicariance patterns and favour dispersal explanations for current biodiversity patterns. © 2013 The Linnean Society of London     

In and out of Madagascar: Dispersal to Peripheral Islands, Insular Speciation and Diversification of Indian Ocean Daisy Trees (Psiadia, Asteraceae)

Madagascar is surrounded by archipelagos varying widely in origin, age and structure. Although small and geologically young, these archipelagos have accumulated disproportionate numbers of unique lineages in comparison to Madagascar, highlighting the role of waif-dispersal and rapid in situ diversification processes in generating endemic biodiversity. We reconstruct the evolutionary and biogeographical history of the genus Psiadia (Asteraceae), a plant genus with near equal numbers of species in Madagascar and surrounding islands. Analyzing patterns and processes of diversification, we explain species accumulation on peripheral islands and aim to offer new insights on the origin and potential causes for diversification in the Madagascar and Indian Ocean Islands biodiversity hotspot. Our results provide support for an African origin of the group, with strong support for non-monophyly. Colonization of the Mascarenes took place by two evolutionary distinct lineages from Madagascar, via two independent dispersal events, each unique for their spatial and temporal properties. Significant shifts in diversification rate followed regional expansion, resulting in co-occurring and phenotypically convergent species on high-elevation volcanic slopes. Like other endemic island lineages, Psiadia have been highly successful in dispersing to and radiating on isolated oceanic islands, typified by high habitat diversity and dynamic ecosystems fuelled by continued geological activity. Results stress the important biogeographical role for Rodrigues in serving as an outlying stepping stone from which regional colonization took place. We discuss how isolated volcanic islands contribute to regional diversity by generating substantial numbers of endemic species on short temporal scales. Factors pertaining to the mode and tempo of archipelago formation and its geographical isolation strongly govern evolutionary pathways available for species diversification, and the potential for successful diversification of dispersed lineages, therefore, appears highly dependent on the timing of arrival, as habitat and resource properties change dramatically over the course of oceanic island evolution.     

Biogeography of ‘tropical Anagallis’ (Myrsinaceae) inferred from nuclear and plastid DNA sequence data

Aim ‘Tropical Anagallis’ corresponds to one of two evolutionary lineages within the genus Anagallis L. Generally, species within this lineage have a limited distribution in (sub‐)tropical regions in Africa or Madagascar. Two species, however, are endemic to South America, and exhibit a trans‐Atlantic disjunction with the rest of the species within the lineage. To investigate this disjunct distribution, as well as other dispersal events, the distribution of extant taxa was used to hypothesize the ancestral area(s) of distribution. Location Africa, Madagascar, Europe and South America. Methods Dispersal–vicariance analysis (DIVA) was used to optimize distribution areas onto parsimony and Bayesian phylogenies based on sequence data from four chloroplast loci and the nuclear internal transcribed spacers (ITS). Results Parsimony analysis gave one most parsimonious tree while Bayesian analysis resulted in a collapsed node due to alternative placements of Anagallis nummularifolia Baker, endemic to Madagascar. Optimization of the present distribution using DIVA, and the most parsimonious tree and six alternative topologies of the Bayesian analysis, show an origin of the lineage in Europe as most likely, although one topology indicates a broader ancestral distribution area. Dispersal to Africa appears to have been a single event, while two parallel dispersal events seem to have resulted in the American as well as Madagascan distributions. Main conclusions The lineage ‘tropical Anagallis’ evolved in Europe and may have been present in the Eocene boreotropical forests, although scarcity of fossils makes assessment of age difficult. Dispersal to South America is proposed to have been via the North Atlantic land bridge, or, more likely, through transport by the North Equatorial Current. Dispersal from Europe to Africa represents a single event, while dispersal to Madagascar from mainland Africa has occurred twice.     

Multiple Miocene Melastomataceae dispersal between Madagascar, Africa and India

Melastomataceae sensu stricto (excluding Memecylaceae) comprise some 3000 species in the neotropics, 1000 in Asia, 240 in Africa, and 230 in Madagascar. Previous family-wide morphological and DNA analyses have shown that the Madagascan species belong to at least three unrelated lineages, which were hypothesized to have arrived by trans-oceanic dispersal. An alternative hypothesis posits that the ancestors of Madagascan, as well as Indian, Melastomataceae arrived from Africa in the Late Cretaceous. This study tests these hypotheses in a Bayesian framework, using three combined sequence datasets analysed under a relaxed clock and simultaneously calibrated with fossils, some not previously used. The new fossil calibration comes from a re-dated possibly Middle or Upper Eocene Brazilian fossil of Melastomeae. Tectonic events were also tentatively used as constraints because of concerns that some of the family's fossils are difficult to assign to nodes in the phylogeny. Regardless of how the data were calibrated, the estimated divergence times of Madagascan and Indian lineages were too young for Cretaceous explanations to hold. This was true even of the oldest ages within the 95% credibility interval around each estimate. Madagascar's Melastomeae appear to have arrived from Africa during the Miocene. Medinilla, with some 70 species in Madagascar and two in Africa, too, arrived during the Miocene, but from Asia. Gravesia, with 100 species in Madagascar and four in east and west Africa, also appears to date to the Miocene, but its monophyly has not been tested. The study afforded an opportunity to compare divergence time estimates obtained earlier with strict clocks and single calibrations, with estimates based on relaxed clocks and different multiple calibrations and taxon sampling.     

Origin and diversification of the endemic Hawaiian tree snails (Achatinellidae: Achatinellinae) based on molecular evidence

Tree snails of the endemic subfamily Achatinellinae comprise a diverse and important component of the Hawaiian fauna. In recent decades anthropogenic impacts have resulted in devastating extinction rates in Hawaiian tree snails. To address long-standing biogeographic, systematic, and evolutionary questions we used cytochrome c oxidase subunit I (COI) gene sequences to reconstruct the phylogeny of 23 extant species spanning the range of the subfamily from five Hawaiian Islands. To investigate family-level relationships, data were analyzed from 11 terrestrial pulmonate families. Although nodal support for monophyly of the endemic Pacific family Achatinellidae and endemic Hawaiian subfamily Achatinellinae was strong, bifurcation order among deeper ingroup nodes was not well-supported by bootstrap resampling. We hypothesize that lineage extinction and rapidity of lineage formation may have rendered evolutionary reconstruction difficult using a standard phylogenetic approach. Use of an optimized evolutionary model, however, improved resolution and recovered three main clades. The diversification pattern inferred contradicts the traditional biogeographic hypothesis of a Maui origin of the achatinelline lineage. Taxa comprising the basal ingroup clade (Achatinella spp.) and seeding lineages for subsequent clades originated on O'ahu. Therefore it appears that the ancestral colonizing species of achatinellines arrived first on O'ahu from an unknown source, and that O'ahu is the Hawaiian origin of the subfamily. Species previously defined by morphological criteria were generally found to be phylogenetically distinct, and the overall colonization pattern follows the island-age progression rule with several instances of generic polyphyly and back-colonization.     

Phylogeny and biogeography of the staghorn fern genus Platycerium (Polypodiaceae, Polypodiidae)

The genus Platycerium is one of the few pantropical epiphytic fern genera with six species in Afro-Madagascar, 8-11 Australasian species, and a single species in tropical South America. Nucleotide sequences of four chloroplast DNA markers are employed to reconstruct the phylogeny of these ferns and to explore their historical biogeography. The data set was designed to resolve conflicting hypotheses on the relationships within the genus that were based on previous phylogenetic studies exploring morphological evidence. Our results suggest a basal split of Platycerium into two well-supported clades. One clade comprises species occurring in Africa, Madagascar, and South America, whereas the second clade contains exclusively Australasian species. The latter clade is further divided into a clade corresponding to P. bifurcatum and its putative segregates and a clade of seven species occurring from Indochina throughout the Malesian region to New Guinea and Australia. The Afro-Madagascan clade includes a clade of two species found in tropical Africa and a clade of four species that includes three species endemic to Madagascar. The single neotropical species of this genus, P. andinum, is nested within the Afro-Madagascan clade but is not closely related to any extant species.     

In or Out-of-Madagascar?—Colonization Patterns for Large-Bodied Diving Beetles (Coleoptera: Dytiscidae)

High species diversity and endemism within Madagascar is mainly the result of species radiations following colonization from nearby continents or islands. Most of the endemic taxa are thought to be descendants of a single or small number of colonizers that arrived from Africa sometime during the Cenozoic and gave rise to highly diverse groups. This pattern is largely based on vertebrates and a small number of invertebrate groups. Knowledge of the evolutionary history of aquatic beetles on Madagascar is lacking, even though this species-rich group is often a dominant part of invertebrate freshwater communities in both standing and running water. Here we focus on large bodied diving beetles of the tribes Hydaticini and Cybistrini. Our aims with this study were to answer the following questions 1) How many colonization events does the present Malagasy fauna originate from? 2) Did any colonization event lead to a species radiation? 3) Where did the colonizers come from—Africa or Asia—and has there been any out-of-Madagascar event? 4) When did these events occur and were they concentrated to any particular time interval? Our results suggest that neither in Hydaticini nor in Cybistrini was there a single case of two or more endemic species forming a monophyletic group. The biogeographical analysis indicated different colonization histories for the two tribes. Cybistrini required at least eight separate colonization events, including the non-endemic species, all comparatively recent except the only lotic (running water) living Cybister operosus with an inferred colonization at 29 Ma. In Hydaticini the Madagascan endemics were spread out across the tree, often occupying basal positions in different species groups. The biogeographical analyses therefore postulated the very bold hypothesis of a Madagascan origin at a very deep basal node within Hydaticus and multiple out-of-Madagascar dispersal events. This hypothesis needs to be tested with equally intense taxon sampling of mainland Africa as for Madagascar.     

Patterns of endemism and species richness in Malagasy cophyline frogs support a key role of mountainous areas for speciation

Cophyline narrow-mouthed frogs (Anura: Microhylidae) are a diverse endemic radiation of Madagascar. Cophylines contain a high proportion of range restricted species and constitute a good model system to understand patterns of evolutionary diversification in tropical ecosystems. We combine spatial and phylogenetic analyses for a near-complete taxon sample to test competing explanations for patterns of species richness (SR) and endemism. Our reconstruction of the phylogeny of cophylines indicates the presence of 22 new species and several instances of nonmonophyly. We found a strong historical signal in current cophyline ranges indicating a high degree of spatial niche conservatism in clade diversification, with clades occurring in the North of Madagascar constituting the most derived in the phylogeny. We identified six positively correlated centers of SR and endemism that can neither be explained by stochastic models such as elevational or latitudinal mid-domain effect, nor by low-elevation river catchments. Instead, the locations of these centers in areas spanning a high altitudinal range in combination with specific climatic parameters support a key role of mountainous areas for speciation of these anurans, although we cannot exclude an influence of habitat loss due to human impact. High conservation priority is ascribed to these areas.     

Mixed evidence for early bursts of morphological evolution in extant clades

Macroevolutionary theory predicts high rates of evolution should occur early in a clade's history as species exploit ecological opportunity. Evidence from the fossil record has shown a high prevalence of early bursts in morphological evolution, but recent work has provided little evidence for early high rates in the evolution of extant clades. Here, I test the prevalence of early bursts in extant data using phylogenetic comparative methods. Existing models are extended to allow a shift from a background Brownian motion (BM) process to an early burst process within subclades of phylogenies, rather than an early burst being applied to an entire phylogenetic tree. This nested early burst model is compared to other modes of evolution that can occur within subclades, such as evolution with a constraint (Ornstein‐Uhlenbeck model) and nested BM rate shift models. These relaxed models are validated using simulations and then are applied to body size evolution of three major clades of amniotes (mammals, squamates and aves) at different levels of taxonomic organization (order, family). Applying these unconstrained models greatly increases the support for early bursts within nested subclades, and so early bursts are the most common model of evolution when only one shift is analysed. However, the relative fit of early burst models is worse than models that allow for multiple shifts of the BM or OU process. No single‐shift or homogenous model is superior to models of multiple shifts in BM or OU evolution, but the patterns shown by these multirate models are generally congruent with patterns expected from early bursts.     

Rates of morphological evolution are correlated with species richness in salamanders

The tempo and mode of species diversification and phenotypic evolution vary widely across the tree of life, yet the relationship between these processes is poorly known. Previous tests of the relationship between rates of phenotypic evolution and rates of species diversification have assumed that species richness increases continuously through time. If this assumption is violated, simple phylogenetic estimates of net diversification rate may bear no relationship to processes that influence the distribution of species richness among clades. Here, we demonstrate that the variation in species richness among plethodontid salamander clades is unlikely to have resulted from simple time-dependent processes, leading to fundamentally different conclusions about the relationship between rates of phenotypic evolution and species diversification. Morphological evolutionary rates of both size and shape evolution are correlated with clade species richness, but are uncorrelated with simple estimators of net diversification that assume constancy of rates through time. This coupling between species diversification and phenotypic evolution is consistent with the hypothesis that clades with high rates of morphological trait evolution may diversify more than clades with low rates. Our results indicate that assumptions about underlying processes of diversity regulation have important consequences for interpreting macroevolutionary patterns.     

An old adaptive radiation of forest dung beetles in Madagascar

Adaptive radiations of mammals have contributed to the exceptionally high levels of biodiversity and endemism in Madagascar. Here we examine the evolutionary history of the endemic dung beetle tribe Helictopleurini (Scarabaeidae) and its relationship to the widely distributed Oniticellini and Onthophagini. Helictopleurini species are dependent on mammals for their resources. We date the single origin of the tribe at 37 to 23 MY ago, indicating overseas colonization of Madagascar. The main radiation occurred concurrently with the main radiations of lemurs. The ancestors of Helictopleurini are inferred to have been coprophagous species inhabiting open habitats. Subsequent evolution has involved a shift into forests, changes in resource use to a more generalized diet, and changes in body size. Four species of the extant 65 species have shifted to use the dung of the recently introduced cattle in open habitats, allowing these species to greatly expand their geographical ranges.     

Reconciling extreme branch length differences: decoupling time and rate through the evolutionary history of filmy ferns

The rate of molecular evolution is not constant across the Tree of Life. Characterizing rate discrepancies and evaluating the relative roles of time and rate along branches through the past are both critical to a full understanding of evolutionary history. In this study, we explore the interactions of time and rate in filmy ferns (Hymenophyllaceae), a lineage with extreme branch length differences between the two major clades. We test for the presence of significant rate discrepancies within and between these clades, and we separate time and rate across the filmy fern phylogeny to simultaneously yield an evolutionary time scale of filmy fern diversification and reconstructions of ancestral rates of molecular evolution. Our results indicate that the branch length disparity observed between the major lineages of filmy ferns is indeed due to a significant difference in molecular evolutionary rate. The estimation of divergence times reveals that the timing of crown group diversification was not concurrent for the two lineages, and the reconstruction of ancestral rates of molecular evolution points to a substantial rate deceleration in one of the clades. Further analysis suggests that this may be due to a genome-wide deceleration in the rate of nucleotide substitution.     

Why is Madagascar special? The extraordinarily slow evolution of pelican spiders (Araneae,Archaeidae)

Although Madagascar is an ancient fragment of Gondwana, the majority of taxa studied thus far appear to have reached the island through dispersal from Cenozoic times. Ancient lineages may have experienced a different history compared to more recent Cenozoic arrivals, as such lineages would have encountered geoclimatic shifts over an extended time period. The motivation for this study was to unravel the signature of diversification in an ancient lineage by comparing an area known for major geoclimatic upheavals (Madagascar) versus other areas where the environment has been relatively stable. Archaeid spiders are an ancient paleoendemic group with unusual predatory behaviors and spectacular trophic morphology that likely have been on Madagascar since its isolation. We examined disparities between Madagascan archaeids and their non‐Madagascan relatives regarding timing of divergence, rates of trait evolution, and distribution patterns. Results reveal an increased rate of adaptive trait diversification in Madagascan archaeids. Furthermore, geoclimatic events in Madagascar over long periods of time may have facilitated high species richness due to montane refugia and stability, rainforest refugia, and also ecogeographic shifts, allowing for the accumulation of adaptive traits. This research suggests that time alone, coupled with more ancient geoclimatic events allowed for the different patterns in Madagascar.     

Phylogenetic analysis of ecomorphological divergence, community structure, and diversification rates in dusky salamanders (Plethodontidae: Desmognathus)

An important dimension of adaptive radiation is the degree to which diversification rates fluctuate or remain constant through time. Focusing on plethodontid salamanders of the genus Desmognathus, we present a novel synthetic analysis of phylogeographic history, rates of ecomorphological evolution and species accumulation, and community assembly in an adaptive radiation. Dusky salamanders are highly variable in life history, body size, and ecology, with many endemic lineages in the southern Appalachian Highlands of eastern North America. Our results show that life-history evolution had important consequences for the buildup of plethodontid-salamander species richness and phenotypic disparity in eastern North America, a global hot spot of salamander biodiversity. The origin of Desmognathus species with aquatic larvae was followed by a high rate of lineage accumulation, which then gradually decreased toward the present time. The peak period of lineage accumulation in the group coincides with evolutionary partitioning of lineages with aquatic larvae into seepage, stream-edge, and stream microhabitats. Phylogenetic simulations demonstrate a strong correlation between morphology and microhabitat ecology independent of phylogenetic effects and suggest that ecomorphological changes are concentrated early in the radiation of Desmognathus. Deep phylogeographic fragmentation within many codistributed ecomorph clades suggests long-term persistence of ecomorphological features and stability of endemic lineages and communities through multiple climatic cycles. Phylogenetic analyses of community structure show that ecomorphological divergence promotes the coexistence of lineages and that repeated, independent evolution of microhabitat-associated ecomorphs has a limited role in the evolutionary assembly of Desmognathus communities. Comparing and contrasting our results to other adaptive radiations having different biogeographic histories, our results suggest that rates of diversification during adaptive radiation are intimately linked to the degree to which community structure persists over evolutionary time.     

Systematic revision of the genus Aglyptodactylus Boulenger, 1919 (Amphibia: Ranidae), and analysis of its phylogenetic relationships to other Madagascan ranid genera (Tomopterna, Boophis, Mantidactylus, and Mantella)

Recent field studies revealed two new species of the genus Aglyptodactylus (Amphibia: Anura: Ranidae), which was hitherto considered as monotypic and confined to humid eastern Madagascar. Both new species, Aglyptodactylus laticeps sp. n. and Aglyptodactylus securifer sp. n. , occur syntopically in the deciduous dry forest of Kirindy in western Madagascar. In comparison to Aglyptodactylus madagascariensis from eastern rainforests, the new species A. laticeps shows a remarkable morphological divergence, which may be partly due to adaptations to burrowing habits in dry environments. Despite of the morphological differentiation, advertisement calls and osteology indicate that all three species of Aglyptodactylus are closely related. A phylogenetic analysis of the Madagascan ranid genera Aglyptodactylus, Mantella, Mantidactylus, Boophis , and Tomopterna (the latter including species from Madagascar, Africa, and Asia) strongly supports a sister group relationship of Aglyptodactylus with the ranine genus Tomopterna . We therefore transfer Aglyptodactylus from the Rhacophorinae to the Raninae and discuss implications of this rearrangement for ranoid systematics. The existence of the endemic genus Aglyptodactylus in Madagascar as well as its close phylogenetic relationships to Tomopterna confirm that the Raninae were already present on the Madagascan plate before its separation from Africa. The Madagascan Tomopterna labrosa shows several important differences both to Asian and to African species of the genus, and is therefore transferred from the subgenus Sphaerotheca (now restricted to Asia) to a new subgenus Laliostoma subgen. n .     

Rates of Dinosaur Body Mass Evolution Indicate 170 Million Years of Sustained Ecological Innovation on the Avian Stem Lineage

Large-scale adaptive radiations might explain the runaway success of a minority of extant vertebrate clades. This hypothesis predicts, among other things, rapid rates of morphological evolution during the early history of major groups, as lineages invade disparate ecological niches. However, few studies of adaptive radiation have included deep time data, so the links between extant diversity and major extinct radiations are unclear. The intensively studied Mesozoic dinosaur record provides a model system for such investigation, representing an ecologically diverse group that dominated terrestrial ecosystems for 170 million years. Furthermore, with 10,000 species, extant dinosaurs (birds) are the most speciose living tetrapod clade. We assembled composite trees of 614–622 Mesozoic dinosaurs/birds, and a comprehensive body mass dataset using the scaling relationship of limb bone robustness. Maximum-likelihood modelling and the node height test reveal rapid evolutionary rates and a predominance of rapid shifts among size classes in early (Triassic) dinosaurs. This indicates an early burst niche-filling pattern and contrasts with previous studies that favoured gradualistic rates. Subsequently, rates declined in most lineages, which rarely exploited new ecological niches. However, feathered maniraptoran dinosaurs (including Mesozoic birds) sustained rapid evolution from at least the Middle Jurassic, suggesting that these taxa evaded the effects of niche saturation. This indicates that a long evolutionary history of continuing ecological innovation paved the way for a second great radiation of dinosaurs, in birds. We therefore demonstrate links between the predominantly extinct deep time adaptive radiation of non-avian dinosaurs and the phenomenal diversification of birds, via continuing rapid rates of evolution along the phylogenetic stem lineage. This raises the possibility that the uneven distribution of biodiversity results not just from large-scale extrapolation of the process of adaptive radiation in a few extant clades, but also from the maintenance of evolvability on vast time scales across the history of life, in key lineages.     

Phylogenetic properties of Tertiary relict flora in the east Asian continental islands: imprint of climatic niche conservatism and in situ diversification

Understanding biodiversity patterns on islands has long been a central aim in ecology and conservation biology. Island‐specific biogeographical processes play substantial roles in the formation of endemic biota. Here, we examined how climate niche conservatism and geohistorical factors are interactively associated with in situ diversification of Tertiary relict flora in the east Asian continental islands. We generated two novel datasets for species distribution and phylogeny that included all of the known vascular plant species in Japan (5575). Then we tested phylogenetic signal of climatic tolerance, in terms of absolute minimum temperature and water balance, and explored environmental predictors of phylogenetic structure (evolutionary derivedness and clustering) of species assemblages. Although phylogenetic signal of climatic tolerance was significant across the phylogeny of most species, the strength of climatic niche conservatism differed among ferns, gymnosperms, angiosperm trees, and angiosperm herbs. For angiosperm trees, cold temperatures acted as environmental filters that generated phylogenetic derivedness/clustering of species assemblages. For fern and angiosperm herb species, however, phylogenetic properties were not associated with climatic harshness. These contrasting patterns among groups reflected climate niche evolution in vascular plants with different growth forms and traits; for example, diversification of angiosperm trees (but not fern and herb) occurred in response to historical climatic cooling. More importantly, geographical constraints contributed to evolutionary radiation that resulted from isolation by distance from the continent or by elevation. Quaternary climate change was also associated with clade‐specific radiation in refugial habitats. The degree to which geographical, geological, and palaeoclimatic variables explain the phylogenetic structure underscores the importance of isolation‐ and habitat‐stability‐related geohistorical processes in driving in situ diversification despite climatic niche conservatism. We propose that the highly endemic flora of the east Asian islands resulted from the interplay of idiosyncratic regional factors, and ecological and evolutionary processes, such as climate niche assembly and adaptive/nonadaptive radiation.     

Multilocus phylogeny of a cryptic radiation of Afrotropical long-fingered bats (Chiroptera,Miniopteridae)

The Old World bat family Miniopteridae comprises only the genus Miniopterus, which includes 20 currently recognized species from the Afrotropical realm and 15 species from Eurasia and Australasia. Since 2003, the number of recognized Miniopterus species has grown from 19 to 35, with most newly described species endemic to Madagascar and the Comoros Archipelago. We investigated genetic variation, phylogenetic relationships and clade membership in Miniopterus focusing on Afrotropical taxa. We generated mitochondrial cytochrome-b (cyt-b) and nuclear intron data (five genes) from 352 vouchered individuals collected at 78 georeferenced localities. Including 99 additional mitochondrial sequences from GenBank, we analysed a total of 25 recognized species. Mitochondrial genetic distances among cyt-b-supported clades averaged 9.3%, representing as many as five undescribed species. Multilocus coalescent delimitation strongly supported the genetic isolation of eight of nine tested unnamed clades. A large number of sampled clades in sub-Saharan Africa are distributed wholly or partly in East Africa (nine of 13 clades), suggesting that Miniopterus diversity has been grossly underestimated. Although 25 of 27 cyt-b and 23 of 25 nuclear gene tree lineages from the Afrotropics were strongly supported as monophyletic, a majority of deep nodes were poorly resolved in phylogenetic analyses. Long terminal branches subtending short backbone internodes in the phylogenetic analyses suggest a rapid radiation model of diversification. This hypothesis needs to be tested using more phylogenetically informative data.