Constant Diversification Rate Research Articles

Diversification and biogeography of Rhacophoridae – a model testing approach

A central focus of evolutionary biology is to understand species diversity by studying how they arrived at their current geographic distributions. The biogeography of the Old World tree frogs in the family Rhacophoridae has been extensively studied suggesting an early Paleogene origin in Asia (out of Asia hypothesis) with alternative hypotheses in play. However, these alternative hypotheses especially considering adjacency of biogeographical regions and plate tectonics have not been tested empirically. Here using a comprehensive time calibrated phylogeny and constrained dispersal multipliers we studied the biogeographical history and diversification of Rhacophoridae, distributed in five biogeographical regions. Five hypotheses suggesting different centers of origin, and additional hypotheses considering adjacency and plate tectonics were tested to delineate the biogeographical history of Rhacophoridae. In addition, various diversification models that accounted for factors such as lineage isolation time, diversity-dependence, paleotemperatures, speciation and extinction rates were also used to test patterns of diversification. Results confirmed an East/Southeast Asian center of origin (out of Asia), with dispersal likely mediated by plate tectonics and adjacency of biogeographical regions, which could be linked to periodic sea level fluctuations and climate changes. The best-fitting diversification models explained diversification through lineage isolation time and paleotemperature regimes, while diversity-dependent models had low support. Speciation was linearly dependent on time and paleotemperatures, while extinction rates were exponentially dependent on time and linearly dependent on paleotemperature. Our findings demonstrate that variable extinction rates contribute towards maintaining a constant diversification rate for rhacophorids. We discuss that episodic major extinction events on the Indian Plate may have played a major role in shaping the early evolution of Rhacophoridae thus favoring an Out of Asia hypothesis in the empirical models. However, current biogeographic models may not be sufficient to explain the origin of Rhacophoridae, as multiple factors are likely at play.

Macroevolutionary dynamics in the transition of angiosperms to aquatic environments.

Summary Angiosperm lineages in aquatic environments are characterized by high structural and functional diversity, and wide distributions. A long‐standing evolutionary riddle is what processes have caused the relatively low diversity of aquatic angiosperms compared to their terrestrial relatives.We use diversification and ancestral reconstruction models with a comprehensive > 10 000 genus angiosperm phylogeny to elucidate the macroevolutionary dynamics associated with transitions of terrestrial plants to water.Our study reveals that net diversification rates are significantly lower in aquatic than in terrestrial angiosperms due to lower speciation and higher extinction. Shifts from land to water started early in angiosperm evolution, but most events were concentrated during the last c. 25 million years. Reversals to a terrestrial habitat started only 40 million years ago, but occurred at much higher rates. Within aquatic angiosperms, the estimated pattern is one of gradual accumulation of lineages, and relatively low and constant diversification rates throughout the Cenozoic.Low diversification rates, together with infrequent water transitions, account for the low diversity of aquatic angiosperms today. The stressful conditions and small global surface of the aquatic habitat available for angiosperms are hypothesized to explain this pattern.

Molecular phylogeny, classification, biogeography and diversification patterns of a diverse group of moths (Geometridae: Boarmiini)

Understanding how and why some groups have become more species-rich than others, and how past biogeography may have shaped their current distribution, are questions that evolutionary biologists have long attempted to answer. We investigated diversification patterns and historical biogeography of a hyperdiverse lineage of Lepidoptera, the geometrid moths, by studying its most species-rich tribe Boarmiini, which comprises ca. 200 genera and ca. known 3000 species. We inferred the evolutionary relationships of Boarmiini based on a dataset of 346 taxa, with up to eight genetic markers under a maximum likelihood approach. The monophyly of Boarmiini is strongly supported. However, the phylogenetic position of many taxa does not agree with current taxonomy, although the monophyly of most major genera within the tribe is supported after minor adjustments. Three genera are synonymized, one new combination is proposed, and four species are placed in incertae sedis within Boarmiini. Our results support the idea of a rapid initial diversification of Boarmiini, which also implies that no major taxonomic subdivisions of the group can currently be proposed. A time-calibrated tree and biogeographical analyses suggest that boarmiines appeared in Laurasia ca. 52 Mya, followed by dispersal events throughout the Australasian, African and Neotropical regions. Most of the transcontinental dispersal events occurred in the Eocene, a period of intense geological activity and rapid climate change. Diversification analyses showed a relatively constant diversification rate for all Boarmiini, except in one clade containing the species-rich genus Cleora. The present work represents a substantial contribution towards understanding the evolutionary origin of Boarmiini moths. Our results, inevitably biased by taxon sampling, highlight the difficulties with working on species-rich groups that have not received much attention outside of Europe. Specifically, poor knowledge of the natural history of geometrids (particularly in tropical clades) limits our ability to identify key innovations underlying the diversification of boarmiines.

Unexpected cryptic species diversity of parasites of the family Xenidae (Strepsiptera) with a constant diversification rate over time

AbstractParasitism is one of the most successful and ancient strategies. Due to the specialized lifestyle of parasites, they are usually affected by reductions and changes in their body plan in comparison with nonparasitic sister groups. Extreme environmental conditions may impose restraints on behavioural or physiological adaptations to a specific host and limit morphological changes associated with speciation. Such morphological homogeneity has led to the diversity of parasites being underestimated in morphological studies. By contrast, the species concept has dramatically changed in many parasitic groups during recent decades of study using DNA sequence data. Here we tested the phenomenon of cryptic species diversity in the twisted‐wing parasite family Xenidae (Strepsiptera) using nuclear and mitochondrial DNA sequence data for a broad sample of Xenidae. We used three quantitative methods of species delimitation from the molecular phylogenetic data – one distance‐based (ABGD) and two tree‐based (GMYC, bPTP). We found 77–96 putative species in our data and suggested the number of Xenidae species to be more diverse than expected. We identified 67 hosts to species level and almost half of them were not previously known as hosts of Xenidae. The mean number of host species per putative species varied between 1.39 and 1.55. The constant rate in net diversification can be explained by the flexibility of this parasitic group, represented by their ability to colonize new host lineages combined with passive long‐range dispersal by hosts.

Molecular phylogeny and historical biogeography of Parnara butterflies (Lepidoptera: Hesperiidae)

The butterfly genus Parnara (Hesperiinae: Baorini), of which some are major pests of economic crops (e.g., rice, wild rice stems and sugarcane), currently consists of 10 species and several subspecies and has a highly disjunct distribution in Australia, Africa, and Asia. We determined the systematic relationships and biogeographical history of the genus by reconstructing the phylogeny based on eight genes and 101 specimens representing all 10 recognized species. Four species delimitation methods (ABGD, bPTP, GMYC and BPP) were also employed to assess the taxonomic status of each species. Based on these results and analyses, we recognize 11 extant species in the genus. The status of the taxon P. naso poutieri (Boisduval, 1833) from Madagascar is revised as a distinct species, Parnara poutieri (Boisduval, 1833) stat. rev. The subspecies P. guttata mangala (Moore, 1866) syn. nov. is synonymized with P. guttata guttata (Bremer & Grey, 1853), while P. bada (Moore, 1878) is provisionally treated as a complex of two species, namely P. bada and P. apostata (Snellen, 1886). The monophyly of Parnara is strongly supported, with the following relationships: P. amalia + ((P. monasi + (P. poutieri + P. naso)) + ((P. kawazoei + P. bada complex) + (P. ganga + (P. ogasawarensis + (P. guttata + P. batta))))). Divergence time and ancestral range estimates indicate that the common ancestor of Parnara originated in an implausible area of Australia, Africa, and Oriental region in the mid-Oligocene and then differentiated in the late Miocene-late Pliocene. Dispersal and range expansion have played an important role in diversification of the genus in Asia and Afica. Relatively stable geotectonic plates at the time when most extant lineages appeared during the late Miocene-early Pliocene might have been the factor responsible for the relatively constant low dynamic rate of diversification within the group.

Diversification of shrub frogs (Rhacophoridae, Pseudophilautus) in Sri Lanka – Timing and geographic context

Pseudophilautus comprises an endemic diversification predominantly associated with the wet tropical regions of Sri Lanka that provides an opportunity to examine the effects of geography and historical climate change on diversification. Using a time-calibrated multi-gene phylogeny, we analyze the tempo of diversification in the context of past climate and geography to identify historical drivers of current patterns of diversity and distribution. Molecular dating suggests that the diversification was seeded by migration across a land-bridge connection from India during a period of climatic cooling and drying, the Oi-1 glacial maximum around the Eocene-Oligocene boundary. Lineage-through-time plots suggest a gradual and constant rate of diversification, beginning in the Oligocene and extending through the late Miocene and early Pliocene with a slight burst in the Pleistocene. There is no indication of an early-burst phase of diversification characteristic of many adaptive radiations, nor were there bursts of diversification associated with favorable climate shifts such as the intensification of monsoons. However, a late Miocene (8.8 MYA) back-migration to India occurred following the establishment of the monsoon. The back migration did not trigger a diversification in India similar to that manifest in Sri Lanka, likely due to occupation of available habitat, and consequent lack of ecological opportunity, by the earlier radiation of a sister lineage of frogs (Raorchestes) with similar ecology. Phylogenetic area reconstructions show a pattern of sister species distributed across adjacent mountain ranges or from different parts of large montane regions, highlighting the importance of isolation and allopatric speciation. Hence, local species communities are composed of species from disparate clades that, in most cases, have been assembled through migration rather than in situ speciation. Lowland lineages are derived from montane lineages. Thus, the hills of Sri Lanka acted as species pumps as well as refuges throughout the 31 million years of evolution, highlighting the importance of tropical montane regions for both the generation and maintenance of biodiversity.

Vicariance versus dispersal across Beringian land bridges to explain circumpolar distribution: A case study in plants with high dispersal potential

AbstractAimTo disentangle the importance of the Beringian land bridges during the Pliocene and Quaternary periods in order to explain the current distribution of circumpolar plants with potential for long‐distance dispersal.LocationCircumpolar (Arctic and Antarctic).MethodsWe sampled all extant species in Carex section Glareosae (26 species and 2 subspecies) and analysed 14 DNA regions, including the nrDNA regions ETS and ITS, three nuclear single‐copy genes (CATP, G3PDH and GZF), and nine cpDNA regions: 5′trnK intron, atpIH, matK, ndhJ‐trnF, psbA‐trnH, rpl32‐trnL, rps16, trnC‐ycf6 and ycf6‐psbM. After testing for outlier proportions, we used Bayesian inference, maximum likelihood and a species‐tree approach to infer phylogenetic relationships between species; divergence times were estimated using Beast2. We then performed biogeographical analyses using “BioGeoBEARS” to estimate ancestral areas by means of reticulate models. Finally, lineage through time (LTT) and diversification pattern analyses were performed using Bamm.ResultsCarex section Glareosae is a monophyletic group that diverged c. 6.56 Ma (4.54–8.51 Ma at 95% highest posterior density interval). We show that within‐area cladogenetic speciation events and anagenetic dispersal (including some vicariance events) play an important role in shaping distribution in species with potential for long‐distance dispersal. Diversification patterns show constant diversification rates over time.Main conclusionsThe Bering Strait may have played an important role in shaping the current distribution of the species in the section, facilitating dispersal between Asia and North America during glacial periods when the Beringian land bridges were open. Nevertheless, we cannot discount long‐distance dispersal as an alternative major force shaping the species distribution in the section.

Aging asexual lineages and the evolutionary maintenance of sex.

Finite populations of asexual and highly selfing species suffer from a reduced efficacy of selection. Such populations are thought to decline in fitness over time due to accumulating slightly deleterious mutations or failing to adapt to changing conditions. These within-population processes that lead nonrecombining species to extinction may help maintain sex and outcrossing through species level selection. Although inefficient selection is proposed to elevate extinction rates over time, previous models of species selection for sex assumed constant diversification rates. For sex to persist, classic models require that asexual species diversify at rates lower than sexual species; the validity of this requirement is questionable, both conceptually and empirically. We extend past models by allowing asexual lineages to decline in diversification rates as they age, that is nonrecombining lineages "senesce" in diversification rates. At equilibrium, senescing diversification rates maintain sex even when asexual lineages, at young ages, diversify faster than their sexual progenitors. In such cases, the age distribution of asexual lineages contains a peak at intermediate values rather than showing the exponential decline predicted by the classic model. Coexistence requires only that the average rate of diversification in asexuals be lower than that of sexuals.

Biogeography and diversification dynamics of the African woodpeckers

The dynamics of species accumulation of African terrestrial vertebrates over time remains underexplored in comparison with those in the New World, despite Africa hosting about 25% of the world’s avian diversity. This lack of knowledge hampers our understanding of the fundamental processes that drive biodiversity and the dynamics of speciation. To begin to address this gap, we reconstructed species-level phylogenies of two unrelated clades of African woodpeckers (12 species of Geocolaptes/Campethera and 13 species of Chloropicus/Mesopicos/Dendropicos/Ipophilus) that diverged from their closest Indo-Malayan relatives at similar times. Our results demonstrate that the current taxonomy is misleading: three (Campethera, Dendropicos and Mesopicos) out of four polytpic genera/subgenera are not monophyletic. Our results also show that current estimates of diversity at the species level are significantly understated, as up to 18 species for the ‘Campethera clade’ and 19 for the ‘Dendropicos clade’ could be recognized. The first splits within both clades involve species that are largely restricted to the Guineo-Congolian biogeographic regions, followed by later adaptations to particular habitats (forest versus savannah) and colonization of other regions (e.g. Southern Africa), each of which occurred multiple times in both clades. Assuming a conservative species delimitation scheme, our results indicate that diversification rates are decreasing through time for both clades. Applying a more extreme species recognition scheme (18 and 19 species for the Campethera and Dendropicos clades, respectively), our results support a decrease in diversification rates only for the Dendropicos clade and thus underline the importance of the number of species included in our diversification analyses. Greater ecological diversity of the Campethera clade where multiple species exhibit either an arboreal or terrestrial foraging strategy might explain the constant diversification rates through time we found under the eighteen species scheme.

Constant diversification rates of endemic gastropods in ancient Lake Ohrid: ecosystem resilience likely buffers environmental fluctuations

Abstract. Ancient lakes represent key ecosystems for endemic freshwater species. This high endemic biodiversity has been shown to be mainly the result of intra-lacustrine diversification. Whereas the principle role of this mode of diversification is generally acknowledged, actual diversification rates in ancient lakes remain little understood. At least four types are conceivable. Diversification rates may be constant over time, they may fluctuate, rates may be higher in the initial phase of diversification, or there may be a pronounced lag phase between colonization and subsequent diversification. As understanding the tempo of diversification in ancient lake environments may help reveal the underlying processes that drive speciation and extinction, we here use the Balkan Lake Ohrid as a model system and the largest species flock in the lake, the non-pyrgulinid Hydrobiidae, as a model taxon to study changes in diversification rates over time together with the respective drivers. Based on phylogenetic, molecular-clock, lineage-through-time plot, and diversification-rate analyses we found that this potentially monophyletic group is comparatively old and that it most likely evolved with a constant diversification rate. Preliminary data of the SCOPSCO (Scientific Collaboration On Past Speciation Conditions in Lake Ohrid) deep-drilling program do indicate signatures of severe environmental/climatic perturbations in Lake Ohrid. However, so far there is no evidence for the occurrence of catastrophic environmental events. We therefore propose that the constant diversification rate observed in endemic gastropods has been caused by two factors: (i) a potential lack of catastrophic environmental events in Lake Ohrid and/or (ii) a probably high ecosystem resilience, buffering environmental changes. Parameters potentially contributing to the lake's high ecosystem resilience are its distinct bathymetry, ongoing tectonic activities, and karst hydrology. The current study not only contributes to one of the overall goals of the SCOPSCO deep-drilling program – inferring the driving forces for biotic evolution in Lake Ohrid. It might also enhance our understanding of how ecosystem resilience, in general, may promote relatively constant diversification rates in isolated ecosystems. However, we encourage future studies testing hypotheses about the lack of catastrophic events in Lake Ohrid. These studies should be based on high-resolution data for the entire geological history of the lake, and they should potentially involve information from the sediment fossil record, not only for gastropods but also for other groups with a high share of endemic taxa.

Shotgun Mitogenomics Provides a Reference Phylogenetic Framework and Timescale for Living Xenarthrans.

Xenarthra (armadillos, sloths, and anteaters) constitutes one of the four major clades of placental mammals. Despite their phylogenetic distinctiveness in mammals, a reference phylogeny is still lacking for the 31 described species. Here we used Illumina shotgun sequencing to assemble 33 new complete mitochondrial genomes, establishing Xenarthra as the first major placental clade to be fully sequenced at the species level for mitogenomes. The resulting data set allowed the reconstruction of a robust phylogenetic framework and timescale that are consistent with previous studies conducted at the genus level using nuclear genes. Incorporating the full species diversity of extant xenarthrans points to a number of inconsistencies in xenarthran systematics and species definition. We propose to split armadillos into two distinct families Dasypodidae (dasypodines) and Chlamyphoridae (euphractines, chlamyphorines, and tolypeutines) to better reflect their ancient divergence, estimated around 42 Ma. Species delimitation within long-nosed armadillos (genus Dasypus) appeared more complex than anticipated, with the discovery of a divergent lineage in French Guiana. Diversification analyses showed Xenarthra to be an ancient clade with a constant diversification rate through time with a species turnover driven by high but constant extinction. We also detected a significant negative correlation between speciation rate and past temperature fluctuations with an increase in speciation rate corresponding to the general cooling observed during the last 15 My. Biogeographic reconstructions identified the tropical rainforest biome of Amazonia and the Guiana Shield as the cradle of xenarthran evolutionary history with subsequent dispersions into more open and dry habitats.

On the historical biogeography of global Galliformes: ancestral range and diversification patterns

In this study, the ancestral distributional ranges and the tempo of diversification patterns of global Galliformes were investigated. Different diversification models characterizing possible tempo patterns were fitted and compared onto the phylogenetic tree for the 197 Galliforme species, consisting of a constant-speciation and constant-extinction model (CONSTANT), a decreasing-speciation and constant-extinction model (SPVAR), a constant-speciation and increasing-extinction model (EXVAR) and a decreasing-speciation and increasing-extinction model (BOTHVAR). Ancestral range reconstruction was conducted using the dispersal-extinction-cladogenesis model. A constant-diversification-rate (CONSTANT) model best quantified the historical speciation patterns of this avian assemblage through model selection. Clade age and species richness are significantly and positively correlated. The most recent common ancestor for Galliformes species was originally found in the disjunctive regions between Southeast Asia and North America. High-frequency dispersal events were identified across the whole evolutionary time. The constant diversification rate for global Galliforme species implied that there were no diversification rate-shifting trends for Galliformes species. The present study may contribute to the understanding of the ecology and diversity patterns of Galliformes from the perspective of historical biogeography, although some limitations existed.

Epiphytic leafy liverworts diversified in angiosperm-dominated forests.

Recent studies have provided evidence for pulses in the diversification of angiosperms, ferns, gymnosperms, and mosses as well as various groups of animals during the Cretaceous revolution of terrestrial ecosystems. However, evidence for such pulses has not been reported so far for liverworts. Here we provide new insight into liverwort evolution by integrating a comprehensive molecular dataset with a set of 20 fossil age constraints. We found evidence for a relative constant diversification rate of generalistic liverworts (Jungermanniales) since the Palaeozoic, whereas epiphytic liverworts (Porellales) show a sudden increase of lineage accumulation in the Cretaceous. This difference is likely caused by the pronounced response of Porellales to the ecological opportunities provided by humid, megathermal forests, which were increasingly available as a result of the rise of the angiosperms.

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.

Diversification patterns and processes of wingless endemic insects in the Mediterranean Basin: historical biogeography of the genusBlaps(Coleoptera: Tenebrionidae)

Aim The Mediterranean Basin (MB) is a species-rich biogeographical region with many endemic taxa. We analysed the historical patterns of temporal and geographical diversification of Mediterranean Blaps (Tenebrionidae), a diverse group of flightless beetles, estimated their date of origin and colonization of the MB, and tracked temporal changes in diversification rates. Location Mediterranean Basin. Methods We reconstructed the phylogenetic relationships of Mediterranean Blaps using four mitochondrial genes and 47 morphological characters. Divergence-time estimates were investigated with a Bayesian relaxed clock approach that was calibrated with both fossil and geological constraints. Biogeographical analyses were performed using the dispersal–extinction–cladogenesis likelihood model associated with a stratified palaeogeographical scenario. Diversification rate analyses allowed the investigation of diversity dynamics through time as well as rate shifts during major Cenozoic climate events. Results The Bayesian relaxed clock analysis suggests that Blaps first appeared in the MB about 28 Ma. The most likely scenario is that Mediterranean Blaps originated in the Arabian and north-east African regions and then dispersed progressively westwards and northwards, using temporary land bridges to colonize the northern shores of the MB. Island endemics are more likely to be the products of recent dispersals than of old vicariance events. Birth–death analyses suggest that diversification rates in the Miocene and Pliocene are consistent with a ‘museum model’, in which most of the extant diversity is best explained by a steady accumulation of lineages under constant diversification rates. Although major Cenozoic climatic events do not seem to have influenced the diversification of Mediterranean Blaps, a decrease in diversification rates was detected during the Pleistocene. Main conclusions Our results suggest that Mediterranean Blaps lineages diversified between the Oligocene and the Pliocene, with current distribution patterns mostly accounted for by early vicariance and late dispersal events. Diversification rates were relatively constant through time, but decreased during Pleistocene glaciation cycles. This scenario may be applicable to other Mediterranean terrestrial animal taxa.

Timetree of Aselloidea Reveals Species Diversification Dynamics in Groundwater

A key challenge for biologists is to document and explain global patterns of diversification in a wide range of environments. Here, we explore patterns of continental-scale diversification in a groundwater species-rich clade, the superfamily Aselloidea (Pancrustacea: Isopoda). Our analyses supported a constant diversification rate during most of the course of Aselloidea evolution, until 4-15 Ma when diversification rates started to decrease. This constant accumulation of lineages challenges the view that groundwater species diversification in temperate regions might have been primarily driven by major changes in physical environment leading to the extinction of surface populations and subsequent synchronous isolation of multiple groundwater populations. Rather than acting synchronously over broad geographic regions, factors causing extinction of surface populations and subsequent reproductive isolation of groundwater populations may act in a local and asynchronous manner, thereby resulting in a constant speciation rate over time. Our phylogeny also revealed several cases of parapatric distributions among closely related surface-water and groundwater species suggesting that species diversification could also arise from a process of disruptive selection along the surface-subterranean environmental gradient. Our results call for re-evaluating the spatial scale and timing of factors causing diversification events in groundwater.

Global ecological pattern of ammonia-oxidizing archaea.

BackgroundThe global distribution of ammonia-oxidizing archaea (AOA), which play a pivotal role in the nitrification process, has been confirmed through numerous ecological studies. Though newly available amoA (ammonia monooxygenase subunit A) gene sequences from new environments are accumulating rapidly in public repositories, a lack of information on the ecological and evolutionary factors shaping community assembly of AOA on the global scale is apparent.Methodology and ResultsWe conducted a meta-analysis on uncultured AOA using over ca. 6,200 archaeal amoA gene sequences, so as to reveal their community distribution patterns along a wide spectrum of physicochemical conditions and habitat types. The sequences were dereplicated at 95% identity level resulting in a dataset containing 1,476 archaeal amoA gene sequences from eight habitat types: namely soil, freshwater, freshwater sediment, estuarine sediment, marine water, marine sediment, geothermal system, and symbiosis. The updated comprehensive amoA phylogeny was composed of three major monophyletic clusters (i.e. Nitrosopumilus, Nitrosotalea, Nitrosocaldus) and a non-monophyletic cluster constituted mostly by soil and sediment sequences that we named Nitrososphaera. Diversity measurements indicated that marine and estuarine sediments as well as symbionts might be the largest reservoirs of AOA diversity. Phylogenetic analyses were further carried out using macroevolutionary analyses to explore the diversification pattern and rates of nitrifying archaea. In contrast to other habitats that displayed constant diversification rates, marine planktonic AOA interestingly exhibit a very recent and accelerating diversification rate congruent with the lowest phylogenetic diversity observed in their habitats. This result suggested the existence of AOA communities with different evolutionary history in the different habitats.Conclusion and SignificanceBased on an up-to-date amoA phylogeny, this analysis provided insights into the possible evolutionary mechanisms and environmental parameters that shape AOA community assembly at global scale.

Diversification of subgenus Calathus (Coleoptera: Carabidae) in the Mediterranean region – glacial refugia and taxon pulses

AbstractAim To investigate the effects of Pleistocene climatic variations on the diversification rate of the subgenus Calathus (Coleoptera: Carabidae), and to estimate the role of vicariance and dispersal for explaining current distributional patterns.Location Western Palaearctic Region, particularly the Mediterranean Basin.Methods Fragments of the mitochondrial cox1–cox2 and the nuclear 28S and EF1α genes were analysed by Bayesian inference. Lineage divergence times were estimated using a Bayesian relaxed molecular clock. Three diversification rate analyses were conducted, namely gamma (γ)‐statistic, birth–death likelihood (BDL) test and survival analyses, in order to test departures from a constant rate model of diversification. A Bayesian approach to dispersal–vicariance analysis was developed to reconstruct the most probable ancestral area of subgenus Calathus and subsequent events of dispersal and colonization.Results A constant rate of speciation events from the late Miocene onwards was found for the subgenus Calathus, whereas recent Pleistocene climatic oscillations played an important role only in shaping intraspecific diversity. Overall diversification patterns for the subgenus are best explained by at least four westward dispersal events from the eastern Mediterranean Basin. Three distinct phylogroups were found for the widely distributed Calathus fuscipes. Incongruence between mitochondrial and nuclear loci was found for a number of species.Main conclusions Diversification analyses suggest either a constant rate of diversification (BDL analysis) or a decrease in diversification rates for the subgenus (survival or γ‐statistics analyses), but not an increase related to the effects of glaciation cycles. Diversification patterns in the subgenus Calathus agree with predictions of the taxon pulse model. From the middle Miocene onwards the Anatolian Peninsula was possibly the main centre of diversification, with successive dispersal events towards the western Mediterranean Basin. Range expansion and secondary contact zones are postulated between members of different phylogroups in C. fuscipes.

Age and historical biogeography of the pantropically distributed Spathelioideae (Rutaceae, Sapindales)

AbstractAim The family Rutaceae (rue family) is the largest within the eudicot order Sapindales and is distributed mainly in the tropical and subtropical regions of both the New World and the Old World, with a few genera in temperate zones. The main objective of this study is to present molecular dating and biogeographical analyses of the subfamily Spathelioideae, the earliest branching clade (which includes eight extant genera), to interpret the temporal and spatial origins of this group, ascertaining possible vicariant patterns and dispersal routes and inferring diversification rates through time.Location Pantropics.Methods A dataset comprising a complete taxon sampling at generic level (83.3% at species level) of Spathelioideae was used for a Bayesian molecular dating analysis (beast). Four fossil calibration points and an age constraint for Sapindales were applied. An ancestral area reconstruction analysis utilizing the dispersal–extinction–cladogenesis model and diversification rate analyses was conducted.Results Dating analyses indicate that Rutaceae and Spathelioideae are probably of Late Cretaceous origin, after which Spathelioideae split into a Neotropical and a Palaeotropical lineage. The Palaeotropical taxa have their origin inferred in Africa, with postulated dispersal events to the Mediterranean, the Canary Islands, Madagascar and Southeast Asia. The lineages within Spathelioideae evolved at a relatively constant diversification rate. However, abrupt changes in diversification rates are inferred from the beginning of the Miocene and during the Pliocene/Pleistocene.Main conclusions The geographical origin of Spathelioideae probably lies in Africa. The existence of a Neotropical lineage may be the result of a dispersal event at a time in the Late Cretaceous when South America and Africa were still quite close to each other (assuming that our age estimates are close to the actual ages), or by Gondwanan vicariance (assuming that our age estimates provide minimal ages only). Separation of land masses caused by sea level changes during the Pliocene and Pleistocene may have been triggers for speciation in the Caribbean genus Spathelia.

Quaternary Climate Change was Not an Engine of Diversification in New World Bats (Chiroptera)

Quaternary climate change has been hypothesized to have played a significant role in driving diversification rates in a variety of taxa. We test the hypothesis of increased rates of diversification during the Quaternary in nine groups of New World bats (Chiroptera). The fit of six models of diversification was determined for each group. None experienced an increase in net diversification, rejecting the Quaternary hypothesis. Instead, four groups experienced constant net diversification rates, suggesting no Quaternary climate change impact. Five groups are evolving under a density-dependent model of diversification, suggesting climate cycles may have reduced rates initiated during the Pliocene or late Miocene. The distribution of divergences between sister taxa is consistent with results obtained from avian lineages experiencing declining rates of Quaternary diversification, further discrediting this often invoked hypothesis. Our results suggest that Quaternary climate change did not increase diversification rates in New World bats.