Changes In Diversification Rates Research Articles

Mammalian faunal change of the Miocene Dove Spring Formation, Mojave region, southern California, USA, in relation to tectonic history

Tectonic processes drive the evolution of basins through local and regional changes in topographic relief, which have long-term effects on mammalian richness and distribution. Mammals respond to the resulting changes in landscape and climate through evolution, shifts in geographic range, and by altering their community composition. Here, we evaluate the relationship between tectonic episodes and the diversification history of fossil mammals in the Miocene Dove Spring Formation (12.5−8.5 Ma) of southern California, USA. This formation contains a rich fossil record of mammals and other vertebrates as well as structural and sedimentological evidence for tectonic episodes of basin extension, rotation, and translation. We used several methods to compare the fossil record to the tectonic history of the Dove Spring Formation. We updated the formation’s geochronology to incorporate current radiometric dating standards and measured additional stratigraphic sections to refine the temporal resolution of large mammal (>1 kg) fossil localities to 200-kyr (or shorter) intervals. Observed species richness over time follows the same trend as the number of localities and specimens, suggesting that richness reflects sampling intensity. Estimates of stratigraphic ranges with 80% confidence intervals were used to conduct per capita diversification analysis and a likelihood approach to changes in faunal composition from one time interval to the next. While edge effects influence time bins at the beginning and end of the study interval, we found changes in diversification rates and faunal composition that are not solely linked to preservation. Several rare species appear at 10.5 Ma and persist through the top of the formation despite variable preservation rates. Changes in faunal composition at 12.1 Ma and 10.5 Ma are not associated with elevated preservation rates, which indicates that some faunal changes are not primarily driven by sampling effort. The lower portion of the formation is characterized by high origination rates and long residence times. The upper portion has high per capita extinction rates that increased in magnitude as basin rotation and translation progressed from 10.5 Ma. The greatest change in faunal composition coincided with basin rotation and translation that interrupted a long-running extensional period. Tectonics played key roles in the diversity of mammals by determining fossil productivity and shaping the landscapes that they inhabited.

Similar diversification patterns in “sky islands”: A comparative approach in lineages from campo rupestre and campo de altitude

Campo rupestre and campo de altitude are two highly diverse plant formations that are found in montane areas in eastern Brazil. These formations are associated with landscapes having different geological histories and are part of different phytogeographic domains under different climatic conditions. It is unclear however, whether lineages in each area have different diversification dynamics and climatic niche evolution. Here we analyze biogeographical history, climatic niche evolution and diversification dynamics of the Cambessedesieae (Melastomataceae), a clade with many endemics in each formation. We use a time-calibrated phylogenetic tree alongside carefully curated distribution points to estimate ancestral ranges and compare diversification dynamics and climatic niche evolution across the group, using models of geographical range evolution (BioGeoBEARS), diversification dynamics (BAMM, GeoSSE) and trait-evolution (l1ou). Our results show that Cambessedesieae is a relatively old (Early Eocene, 48 Mya) clade in comparison to other lineages of similar distribution. An initial split between lineages that are mainly endemic to either formation happened earlier, but, surprisingly, these two lineages have similar diversification dynamics and climatic niche evolution. Shifts in climatic regimes in extant lineages occurred more recently and are not associated with changes in diversification rates. Overall, we show that lineages endemic to montane areas and having different geological histories and in different climatic and phytogeographic contexts can have similar diversification patterns.

CRABS: Congruent rate analyses in birth–death scenarios

Abstract Diversification rates inferred from phylogenies are not identifiable if the rates are allowed to vary freely over time. There are infinitely many combinations of speciation and extinction rate functions that have the exact same likelihood score for a given phylogeny, building a congruence class. The specific shape and characteristics of such congruence classes have not yet been studied. Whether speciation and extinction rate functions within a congruence class share common features is also not known. Prior hypotheses typically render diversification rates identifiable, but the results then depend on these a priori hypotheses and assumptions. To test the robustness of diversification results to these a priori hypotheses, we use two different approaches to explore congruence classes: (i) constructing congruent models under alternative hypotheses and (ii) sampling alternative rate function within the congruence class. Our methods are implemented in the open‐source R package CRABS (https://github.com/afmagee/CRABS). CRABS provides a flexible approach to explore the congruence class and provides summaries of rate functions within a congruence class. The summaries can highlight common trends, that is, increasing, flat or decreasing rates. Although there are infinitely many equally likely diversification rate functions, these can share common features. CRABS can be used to assess if diversification rate patterns are robust despite the non‐identifiability of the birth–death model. In our example, we clearly identify three phases of diversification rate changes that are common among all models which we sampled from the congruence class. Thus, congruence classes are not necessarily a problem for studying historical patterns of biodiversity from phylogenies.

Drivers of diversification in freshwater gastropods vary over deep time.

Unravelling the drivers of species diversification through geological time is of crucial importance for our understanding of long-term evolutionary processes. Numerous studies have proposed different sets of biotic and abiotic controls of speciation and extinction rates, but typically they were inferred for a single, long geological time frame. However, whether the impact of biotic and abiotic controls on diversification changes over time is poorly understood. Here, we use a large fossil dataset, a multivariate birth–death model and a comprehensive set of biotic and abiotic predictors, including a new index to quantify tectonic complexity, to estimate the drivers of diversification for European freshwater gastropods over the past 100 Myr. The effects of these factors on origination and extinction are estimated across the entire time frame as well as within sequential time windows of 20 Myr each. Our results find support for temporal heterogeneity in the factors associated with changes in diversification rates. While the factors impacting speciation and extinction rates vary considerably over time, diversity-dependence and topography are consistently important. Our study highlights that a high level of heterogeneity in diversification rates is best captured by incorporating time-varying effects of biotic and abiotic factors.

Phylotranscriptomic insights into Asteraceae diversity, polyploidy, and morphological innovation.

Biodiversity is not evenly distributed among related groups, raising questions about the factors contributing to such disparities. The sunflower family (Asteraceae, >26,000 species) is among the largest and most diverse plant families, but its species diversity is concentrated in a few subfamilies, providing an opportunity to study the factors affecting biodiversity. Phylotranscriptomic analyses here of 244 transcriptomes and genomes produced a phylogeny with strong support for the monophyly of Asteraceae and the monophyly of most subfamilies and tribes. This phylogeny provides a reference for detecting changes in diversification rates and possible factors affecting Asteraceae diversity, which include global climate shifts, whole-genome duplications (WGDs), and morphological evolution. The origin of Asteraceae was estimated at ~83 Mya, with most subfamilies having diverged before the Cretaceous-Paleocene boundary. Phylotranscriptomic analyses supported the existence of 41 WGDs in Asteraceae. Changes to herbaceousness and capitulescence with multiple flower-like capitula, often with distinct florets and scaly pappus/receptacular bracts, are associated with multiple upshifts in diversification rate. WGDs might have contributed to the survival of early Asteraceae by providing new genetic materials to support morphological transitions. The resulting competitive advantage for adapting to different niches would have increased biodiversity in Asteraceae.

Concordance of HIV transmission risk factors elucidated using viral diversification rate and phylogenetic clustering.

Background and objectivesAlthough HIV sequence clustering is routinely used to identify subpopulations experiencing elevated transmission, it over-simplifies transmission dynamics and is sensitive to methodology. Complementarily, viral diversification rates can be used to approximate historical transmission rates. Here, we investigated the concordance and sensitivity of HIV transmission risk factors identified by phylogenetic clustering, viral diversification rate, changes in viral diversification rate and a combined approach.MethodologyViral sequences from 9848 people living with HIV in British Columbia, Canada, sampled between 1996 and February 2019, were used to infer phylogenetic trees, from which clusters were identified and viral diversification rates of each tip were calculated. Factors associated with heightened transmission risk were compared across models of cluster membership, viral diversification rate, changes in diversification rate, and viral diversification rate among clusters.ResultsViruses within larger clusters had higher diversification rates and lower changes in diversification rate than those within smaller clusters; however, rates within individual clusters, independent of size, varied widely. Risk factors for both cluster membership and elevated viral diversification rate included being male, young, a resident of health authority E, previous injection drug use, previous hepatitis C virus infection or a high recent viral load. In a sensitivity analysis, models based on cluster membership had wider confidence intervals and lower concordance of significant effects than viral diversification rate for lower sampling rates.Conclusions and implicationsViral diversification rate complements phylogenetic clustering, offering a means of evaluating transmission dynamics to guide provision of treatment and prevention services.Lay SummaryUnderstanding HIV transmission dynamics within clusters can help prioritize public health resource allocation. We compared socio-demographic and clinical risk factors associated with phylogenetic cluster membership and viral diversification rate, a historical branching rate, in order to assess their relative concordance and sampling sensitivity.

Ecological opportunity enabled invertebrate radiations in ancient Lake Ohrid

Ancient Lake Ohrid is the oldest and biologically most diverse freshwater lake in Europe. The recent deep-drilling campaign SCOPSCO provided detailed insights into the lake’s limnological history over the past 1.36 my. However, it remains unclear what factors triggered the onset of radiations and whether diversification rates remained constant throughout their evolution. We therefore inferred time-calibrated molecular phylogenies for eight invertebrate groups endemic to Lake Ohrid and performed diversification-rate analyses for the four most species-rich groups. The molecular-clock analyses indicate that few groups possibly originated in springs or rivers in the ‘proto-Balkans’ during the pre-lake phase. The onset of all other radiations, however, can be correlated to one of the three limnological phases in the Ohrid Graben and in Lake Ohrid since 1.9 mya. We therefore assume that the onset of radiations was triggered by an increased ecological opportunity arising from massive environmental changes in the course of the lake deepening. The diversification-rate analyses further indicate that the groups examined diversified with a constant rate. Although the reconstruction of the early evolutionary history of these groups remains challenging, our data suggest that the relatively stable conditions in Lake Ohrid together with its high buffer capacity likely prevented significant changes in diversification rates over time.

Evolution and classification of figs (Ficus, Moraceae) and their close relatives (Castilleae) united by involucral bracts

AbstractFigs and fig wasps are a classic example of an obligate pollination mutualism. Decades of work untangling the ecology and evolution of these organisms has simultaneously contributed to development of the fields of mutualism, coevolution and plant–insect interactions at large. With > 800 species, figs (Ficus, Moraceae) are among some of the larger genera of angiosperms. Phylogenetic studies of Moraceae have supported the clade Castilleae as the sister lineage of Ficus. Compared to Ficus, Castilleae have many fewer species (60 species in 11 genera), suggesting changes in rates of diversification along these two branches. Relatively little is known about Castilleae compared to Ficus, and we argue that defining the clade comprising Ficus and Castilleae, hereafter Involucrata, focuses attention on opportunities for comparative studies of pollination mutualisms and diversification rates. In this study, we define Involucrata and propose a revised classification scheme that accounts for the phylogenetic reconstruction based on the most comprehensive sampling of this group to date. Moving forward, this classification will better guide and support evolutionary, ecological and comparative pollination biology studies of this group.

Biogeography and early diversification of Tapinotaspidini oil-bees support presence of Paleocene savannas in South America

Worldwide distributed tropical savannas were established only in the Miocene, with climatic cooling and rise of C4 grasses. However, there is evidence for an earlier presence of savanna-like vegetation in southern parts of South America. Here we investigated the biogeographic history of a clade of solitary bees which have endemic groups in areas covered by savannas and other types of open vegetation as well as forested areas. We hypothesized that these bees originated in savanna-like biomes and that shifts to forested areas and floral host shifts increased species diversification along their evolutionary history. We reconstructed a comprehensive phylogeny for Tapinotaspidini bees based majorly on original DNA sequences. We then used macroevolutionary tools to estimate ancestral range area and reconstructed ancestral habitat (open versus forested) and host plant association to analyze the effects of shifts in vegetation type and flower hosts on their diversification. Tapinotaspidini bees originated in the Paleocene and in a savanna-type, Cerrado-like, which is reinforced by reconstruction of open vegetation as the most probable ancestral area, thus bringing additional evidence to a much earlier origin of this vegetation type in South America. Shifts to forested areas occurred at least three times in a period of 30 Ma and were responsible for slight increases in diversification rates. Malpighiaceae is the ancestral floral host; host broadening occurred only in the Miocene and at least in three occasions. Host shifts, i.e. from Malpighiaceae to other oil families, occurred in the Eocene and Miocene. Both host broadening and host shifts did not significantly alter diversification rates, however exploitation of other oil sources were important in occupying new habitats. The link between biomes and host plant shifts and changes in diversification rate brings us additional insights into the evolution of bees and associated flora in South America.

Accelerated diversifications in three diverse families of morphologically complex lichen-forming fungi link to major historical events

Historical mass extinction events had major impacts on biodiversity patterns. The most recent and intensively studied event is the Cretaceous – Paleogene (K-Pg) boundary (ca. 66 million years ago [MYA]). However, the factors that may have impacted diversification dynamics vary across lineages. We investigated the macroevolutionary dynamics with a specific focus on the impact of major historical events such as the K-Pg mass extinction event on two major subclasses – Lecanoromycetidae and Ostropomycetidae – of lichen-forming fungi and tested whether variation in the rate of diversification can be associated with the evolution of a specific trait state - macrolichen. Our results reveal accelerated diversification events in three families of morphologically complex lichen-forming fungi – Cladoniaceae, Parmeliaceae, and Peltigeraceae – which are from the subclass Lecanoromycetidae and mostly composed of macrolichens, those that form three dimensional structures. Our RTT plot result for the subclass Lecanoromycetidae also reveals accelerated diversification. Changes in diversification rates occurred around the transition between Mesozoic and Cenozoic eras and was likely related to the K-Pg mass extinction event. The phylogenetic positions for rate increases estimated based on marginal shift probability are, however, scattered from 100 to 40 MYA preventing us from making explicit inference. Although we reveal that the phenotypic state of macrolichens is associated with a higher diversification rate than microlichens, we also show that the evolution of macrolichens predated the K-Pg event. Furthermore, the association between macrolichens and increased diversification is not universal and can be explained, in part, by phylogenetic relatedness. By investigating the macroevolutionary dynamics of lichen-forming fungi our study provides a new empirical system suitable to test the effect of major historical event on shaping biodiversity patterns and to investigate why changes in biodiversity patterns are not in concordance across clades. Our results imply that multiple historical events during the transition from Mesozoic to Cenozoic eras, including the K-Pg mass extinction event, impacted the evolutionary dynamics in lichen-forming fungi. However, future studies focusing on individual lichen-forming fungal families are required to ascertain whether diversification rates are associated with growth form and certain geological events.

A model with many small shifts for estimating species-specific diversification rates

Understanding how and why diversification rates vary through time and space and across species groups is key to understanding the emergence of today's biodiversity. Phylogenetic approaches aimed at identifying variations in diversification rates during the evolutionary history of clades have focused on exceptional shifts subtending evolutionary radiations. While such shifts have undoubtedly affected the history of life, identifying smaller but more frequent changes is important as well. We developed ClaDS-a new Bayesian approach for estimating branch-specific diversification rates on a phylogeny that relies on a model with changes in diversification rates at each speciation event. We show, using Monte Carlo simulations, that the approach performs well at inferring both small and large changes in diversification. Applying our approach to bird phylogenies covering the entire avian radiation, we find that diversification rates are remarkably heterogeneous within evolutionarily restricted species groups. Some groups such as Accipitridae (hawks and allies) cover almost the full range of speciation rates found across the entire bird radiation. As much as 76% of the variation in branch-specific rates across this radiation is due to intraclade variation, suggesting that a large part of the variation in diversification rates is due to many small, rather than few large, shifts.

Anatomy of a Neotropical insect radiation

BackgroundMuch evolutionary theory predicts that diversity arises via both adaptive radiation (diversification driven by selection against niche-overlap within communities) and divergence of geographically isolated populations. We focus on tropical fruit flies (Blepharoneura, Tephritidae) that reveal unexpected patterns of niche-overlap within local communities. Throughout the Neotropics, multiple sympatric non-interbreeding populations often share the same highly specialized patterns of host use (e.g., flies are specialists on flowers of a single gender of a single species of host plants). Lineage through time (LTT) plots can help distinguish patterns of diversification consistent with ecologically limited adaptive radiation from those predicted by ecologically neutral theories. Here, we use a time-calibrated phylogeny of Blepharoneura to test the hypothesis that patterns of Blepharoneura diversification are consistent with an “ecologically neutral” model of diversification that predicts that diversification is primarily a function of time and space.ResultsThe Blepharoneura phylogeny showed more cladogenic divergence associated with geography than with shifts in host-use. Shifts in host-use were associated with ~ 20% of recent splits (< 3 Ma), but > 60% of older splits (> 3 Ma). In the overall tree, gamma statistic and maximum likelihood model fitting showed no evidence of diversification rate changes though there was a weak signature of slowing diversification rate in one of the component clades.ConclusionsOverall patterns of Blepharoneura diversity are inconsistent with a traditional explanation of adaptive radiation involving decreases in diversification rates associated with niche-overlap. Sister lineages usually use the same host-species and host-parts, and multiple non-interbreeding sympatric populations regularly co-occur on the same hosts. We suggest that most lineage origins (phylogenetic splits) occur in allopatry, usually without shifts in host-use, and that subsequent dispersal results in assembly of communities composed of multiple sympatric non-interbreeding populations of flies that share the same hosts.

Impact of whole-genome duplication events on diversification rates in angiosperms.

Polyploidy or whole-genome duplication (WGD) pervades the evolutionary history of angiosperms. Despite extensive progress in our understanding of WGD, the role of these events in promoting diversification is still not well understood. We seek to clarify the possible association between WGD and diversification rates in flowering plants. Using a previously published phylogeny spanning all land plants (31,749 tips) and WGD events inferred from analyses of the 1000 Plants (1KP) transcriptome data, we analyzed the association of WGDs and diversification rates following numerous WGD events across the angiosperms. We used a stepwise AIC approach (MEDUSA), a Bayesian mixture model approach (BAMM), and state-dependent diversification analyses (MuSSE) to investigate patterns of diversification. Sister-clade comparisons were used to investigate species richness after WGDs. Based on the density of 1KP taxon sampling, 106 WGDs were unambiguously placed on the angiosperm phylogeny. We identified 334-530 shifts in diversification rates. We found that 61 WGD events were tightly linked to changes in diversification rates, and state-dependent diversification analyses indicated higher speciation rates for subsequent rounds of WGD. Additionally, 70 of 99 WGD events showed an increase in species richness compared to the sister clade. Forty-six of the 106 WGDs analyzed appear to be closely associated with upshifts in the rate of diversification in angiosperms. Shifts in diversification do not appear more likely than random within a four-node lag phase following a WGD; however, younger WGD events are more likely to be followed by an upshift in diversification than older WGD events.

Phylogenetic estimates of diversification rate are affected by molecular rate variation.

Molecular phylogenies are increasingly being used to investigate the patterns and mechanisms of macroevolution. In particular, node heights in a phylogeny can be used to detect changes in rates of diversification over time. Such analyses rest on the assumption that node heights in a phylogeny represent the timing of diversification events, which in turn rests on the assumption that evolutionary time can be accurately predicted from DNA sequence divergence. But there are many influences on the rate of molecular evolution, which might also influence node heights in molecular phylogenies, and thus affect estimates of diversification rate. In particular, a growing number of studies have revealed an association between the net diversification rate estimated from phylogenies and the rate of molecular evolution. Such an association might, by influencing the relative position of node heights, systematically bias estimates of diversification time. We simulated the evolution of DNA sequences under several scenarios where rates of diversification and molecular evolution vary through time, including models where diversification and molecular evolutionary rates are linked. We show that commonly used methods, including metric-based, likelihood and Bayesian approaches, can have a low power to identify changes in diversification rate when molecular substitution rates vary. Furthermore, the association between the rates of speciation and molecular evolution rate can cause the signature of a slowdown or speedup in speciation rates to be lost or misidentified. These results suggest that the multiple sources of variation in molecular evolutionary rates need to be considered when inferring macroevolutionary processes from phylogenies.

The environmental and evolutionary history of Lake Ohrid (FYROM/Albania): interim results from the SCOPSCO deep drilling project

Abstract. This study reviews and synthesises existing information generated within the SCOPSCO (Scientific Collaboration on Past Speciation Conditions in Lake Ohrid) deep drilling project. The four main aims of the project are to infer (i) the age and origin of Lake Ohrid (Former Yugoslav Republic of Macedonia/Republic of Albania), (ii) its regional seismotectonic history, (iii) volcanic activity and climate change in the central northern Mediterranean region, and (iv) the influence of major geological events on the evolution of its endemic species. The Ohrid basin formed by transtension during the Miocene, opened during the Pliocene and Pleistocene, and the lake established de novo in the still relatively narrow valley between 1.9 and 1.3 Ma. The lake history is recorded in a 584 m long sediment sequence, which was recovered within the framework of the International Continental Scientific Drilling Program (ICDP) from the central part (DEEP site) of the lake in spring 2013. To date, 54 tephra and cryptotephra horizons have been found in the upper 460 m of this sequence. Tephrochronology and tuning biogeochemical proxy data to orbital parameters revealed that the upper 247.8 m represent the last 637 kyr. The multi-proxy data set covering these 637 kyr indicates long-term variability. Some proxies show a change from generally cooler and wetter to drier and warmer glacial and interglacial periods around 300 ka. Short-term environmental change caused, for example, by tephra deposition or the climatic impact of millennial-scale Dansgaard–Oeschger and Heinrich events are superimposed on the long-term trends. Evolutionary studies on the extant fauna indicate that Lake Ohrid was not a refugial area for regional freshwater animals. This differs from the surrounding catchment, where the mountainous setting with relatively high water availability provided a refuge for temperate and montane trees during the relatively cold and dry glacial periods. Although Lake Ohrid experienced significant environmental change over the last 637 kyr, preliminary molecular data from extant microgastropod species do not indicate significant changes in diversification rate during this period. The reasons for this constant rate remain largely unknown, but a possible lack of environmentally induced extinction events in Lake Ohrid and/or the high resilience of the ecosystems may have played a role.

The true tempo of evolutionary radiation and decline revealed on the Hawaiian archipelago.

Establishing the relationship between rates of change in species richness and biotic and abiotic environmental change is a major goal of evolutionary biology. Although exquisite fossil and geological records provide insight in rare cases, most groups lack high-quality fossil records. Consequently, biologists typically rely on molecular phylogenies to study the diversity dynamics of clades, usually by correlating changes in diversification rate with environmental or trait shifts. However, inferences drawn from molecular phylogenies can be limited owing to the challenge of accounting for extinct species, making it difficult to accurately determine the underlying diversity dynamics that produce them. Here, using a geologically informed model of the relationship between changing island area and species richness for the Hawaiian archipelago, we infer the rates of species richness change for 14 endemic groups over their entire evolutionary histories without the need for fossil data, or molecular phylogenies. We find that these endemic clades underwent evolutionary radiations characterized by initially increasing rates of species accumulation, followed by slow-downs. In fact, for most groups on most islands, their time of evolutionary expansion has long past, and they are now undergoing previously unrecognized long-term evolutionary decline. Our results show how landscape dynamism can drive evolutionary dynamics over broad timescales, including driving species loss that is not readily detected using molecular phylogenies, or without a rich fossil record. We anticipate that examination of other clades where the relationship between environmental change and species richness change can be quantified will reveal that many other living groups have also experienced similarly complex evolutionary trajectories, including long-term and ongoing evolutionary decline.

Continental gateways and the dynamics of mammalian faunas

Continental gateways occur where mountainous topography interacts with changing climate and sea level to open or close dispersal corridors. The interaction of permeable or impermeable montane barriers with changing or stable climate yields four biogeographic states, each associated with changes in diversification rates and ecological structure of faunas. For example, permeable montane barriers and climatic stability result in low rates of immigration and extinction, elevated endemic speciation, and stable ecological structure. Three examples from the mammalian fossil record test these scenarios. (1) In Miocene faunas of Pakistan, immigration rates peaked and faunal proportions changed during an interval of cooling and open corridors. (2) In Miocene faunas of Spain, elevated extinction and origination rates and changing trophic structure occurred during regional aridification with open corridors. (3) In Quaternary faunas of South Africa, ungulates experienced range reductions and elevated extinction during the transition from glacial to interglacial climates as corridors closed.

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.

Range expansion and habitat shift triggered elevated diversification of the rice genus (Oryza, Poaceae) during the Pleistocene.

BackgroundThe rice genus (Oryza) contains many wild genetic resources that are vital to the well-being of humans. However, little is known about the process by which the genus diversified or the factors that drove its speciation. Here, we integrated the phylogenetic, molecular dating and biogeographic methods to investigate the spatial-temporal patterns of Oryza diversification, and used a series of model tests to examine whether intercontinental migrations and/or key innovations were associated with significant changes in diversification rates in the genus.ResultsOryza became differentiated in tropical Asia in the Miocene. There were two migrations from the ancestral area into Africa and Australia during the Miocene. We inferred at least 10 migration events out of tropical Asia since the Pleistocene, mainly involving the species adapting open habitat. A rapid increase in diversification rates of the whole Oryza occurred during the Pleistocene. Intercontinental migrations from tropical Asia to other tropical regions were positively correlated with shift in habitat, but not with changes in life history. A habitat preference shift from shade tolerant to open habitat predated the burst in diversification rates.ConclusionsRice species may have been pre-adapted to invade open habitat. Significant increase in diversification rates occurred during the Pleistocene and is associated with range expansion and habitat shift, but not with life history. The rice genus provides an excellent case supporting the idea that range expansion and invasion of novel habitats can drive the diversification of a group.Electronic supplementary materialThe online version of this article (doi:10.1186/s12862-015-0459-1) contains supplementary material, which is available to authorized users.

As old as the mountains: the radiations of the Ericaceae.

Mountains are often more species-rich than lowlands. This could be the result of migration from lowlands to mountains, of a greater survival rate in mountains, or of a higher diversification rate in mountains. We investigated this question in the globally distributed family Ericaceae, which includes c. 4426 species ranging from sea level to >5000m. We predict that the interaction of low specific leaf area (SLA) and montane habitats is correlated with increased diversification rates. A molecular phylogeny of Ericaceae based on rbcL and matK sequence data was built and dated with 18 fossil calibrations and divergence time estimates. We identified radiations using bamm and correlates of diversification rate changes using binary-state speciation and extinction (BiSSE) and multiple-state speciation and extinction (MuSSE) analyses. Analyses revealed six largely montane radiations. Lineages in mountains diversified faster than nonmountain lineages (higher speciation rate, but no difference in extinction rate), and lineages with low SLA diversified faster than high-SLA lineages. Further, habitat and trait had a positive interactive effect on diversification. Our results suggest that the species richness in mountains is the result of increased speciation rather than reduced extinction or increased immigration. Increased speciation in Ericaceae was facilitated by low SLA.