- Research article
- Open Access
Diversity dynamics in New Caledonia: towards the end of the museum model?
BMC Evolutionary Biology volume 11, Article number: 254 (2011)
The high diversity of New Caledonia has traditionally been seen as a result of its Gondwanan origin, old age and long isolation under stable climatic conditions (the museum model). Under this scenario, we would expect species diversification to follow a constant rate model. Alternatively, if New Caledonia was completely submerged after its breakup from Gondwana, as geological evidence indicates, we would expect species diversification to show a characteristic slowdown over time according to a diversity-dependent model where species accumulation decreases as space is filled.
We reanalyze available datasets for New Caledonia and reconstruct the phylogenies using standardized methodologies; we use two ultrametrization alternatives; and we take into account phylogenetic uncertainty as well as incomplete taxon sampling when conducting diversification rate constancy tests. Our results indicate that for 8 of the 9 available phylogenies, there is significant evidence for a diversification slowdown. For the youngest group under investigation, the apparent lack of evidence of a significant slowdown could be because we are still observing the early phase of a logistic growth (i.e. the clade may be too young to exhibit a change in diversification rates).
Our results are consistent with a diversity-dependent model of diversification in New Caledonia. In opposition to the museum model, our results provide additional evidence that original New Caledonian biodiversity was wiped out during the episode of submersion, providing an open and empty space facilitating evolutionary radiations.
New Caledonia is one of the 10 original biodiversity hotspots [1, 2]. Indeed, New Caledonian biodiversity is exceptional for an archipelago of its size (only 19 000 km2) [3–5] and also very distinct  with a level of endemism of seventy-seven percent at the species level and fifteen percent at the generic level for plants [7, 8]. There has been considerable debate about the origin of New Caledonia's tremendous biodiversity [9, 10] and molecular phylogenies of extant taxa have provided a useful window into the tempo and mode of species diversification [11, 12]. With the growth of phylogenetic studies in New Caledonia , we now have a framework to study temporal diversification patterns in the area. Rather than focusing solely on molecular dating techniques, we here investigate how information on diversity dynamics can be used to test the two fundamental models invoked to explain New Caledonian biodiversity.
Due to its Gondwanan continental origin, its long isolation from neighbouring landmasses (like New Zealand or Australia, Figure 1) and its supposed climatic stability, the museum model [14, 15] has classically been invoked to explain the origin of New Caledonian biodiversity . According to this classical view, the slow and gradual accumulation of species from ancient Gondwanan stock with low or absent extinction could explain the high level of species richness on the island . Under this scenario, we would expect biodiversity to follow an exponential model of diversification (Figure 1) where per-lineage rates of speciation and extinction have been constant with no upper limit on clade diversity [17, 18]. This model specifically refers to the old age of the territory to explain the high level of biodiversity. It is thus based on the premise that species richness is coupled with clade age, meaning that old clades on average have more species than young ones.
As opposed to this classical view, the geology of the territory indicates a complete submersion of the island for 20 Ma (from 65 to 45 Ma) following its breakup from the eastern margin of Gondwana (c. 80 Ma) and the presence of an island on the New Caledonia Ridge has only been established since the Late Eocene (around 37 Ma) . All endemic Gondwanan species would have gone extinct and current diversity would have descended from later colonists, whether from nearby island refugia or from long-distance dispersal . This scenario implies a novel ecological space that is open and available, thus facilitating evolutionary radiations [12, 20]. Under this 'ecological opportunity' model , as time passes and diversification progresses, the geographical and ecological space becomes increasingly saturated with fewer opportunities for speciation [22, 23] resulting in a slowdown of diversification rates through time. Under such a scenario, we would expect species diversification to follow a typical niche-filling model [24–26] where the probability of speciation and/or extinction should vary inversely with the number of species, according to a diversity-dependent process [27–30]. We will use the term diversity-dependence  rather than density-dependence [31, 32] because this process refers to the density of species (diversity) rather than the density of individuals .
In this paper, we present the First comparative analysis of species diversification in New Caledonia. Our goal is to estimate diversification dynamic parameters in order to test the two models classically invoked to explain New Caledonia's exceptional biodiversity. We used various groups of angiosperms, lizards, harvestmen, caddisflies and diving beetles, and tested diversification models using the gamma statistic  and likelihood models .
Our statistics-based results (Table 1; Figure 1) show that only three groups out of nine did not have a significantly negative γ: Gracilipsodes, Helicopha and Xanthochorema, suggesting that for most of the studies, a constant rate could be rejected. All the groups with significantly negative γ also passed the MCCR test. A recent study showed that the γ test does not necessarily detect early bursts of diversification  and that model based approaches might be more appropriate for investigating diversity dynamics. Our model-based results show that only the diversification of one group is best explained by a constant rate model: Helicopha. For all the remaining groups, the model-based approach shows a significant positive ΔAIC indicating a better fit to rate-variable models, each time with an inferred slowdown in diversification rates through time. In one case, Agmina, a Yule 2-rate process model was inferred as the best-fit model. In all the remaining cases (7 out of 9), the best fitted model was a linear variant of the diversity-dependent model (DDL), though with p = 0.08 for the bayesian analysis of Papuadytes and p = 0.06 for the bayesian analysis of Gracilipsodes. More complex models (SPVAR, EXVAR and BOTHVAR) allowing a non-zero probability of extinction did not provide a better fit. For our studies, there is also a clear decoupling between clade age and clade size (Pearson's r = 0.22).
Biases towards an apparent slowdown
Diversification analyses are sensitive to biases in the phylogenetic reconstruction method . For example, multiple substitutions could lead to saturation of genetic distances producing incorrectly short branch lengths deeper in the tree . We chose the GTR model because it is the most common and general model for real world DNA. While many authors have used the GTR + I + Γ to incorporate rate heterogeneity , it is well established  that adding a proportion of invariable sites creates a strong correlation between p0 (parameter of I) and α (parameter of Γ), making it impossible to estimate both parameters reliably [41, 42]. Following RAxML's manual recommendations, we used a GTR + Γ model  applied to each partition. This should ensure that our results are not biased by under-parameterization of our phylogenetic reconstruction.
The method of phylogenetic ultrametrization could also influence the estimate of γ [43–45]. In this study we used two different methods: First, maximum likelihood (with RAxML for phylogenetic inference and R8S for ultrametrization) and secondly, bayesian inference (with BEAST). R8S uses an autocorrelated relaxed molecular clock while BEAST uses a non-correlated clock. This should ensure that our results (which were consistent whichever method was used) are not biased by ultrametrization techniques. Incomplete taxon sampling can also introduce some bias in favor of a pattern of slowdown of diversification rates and towards a more negative γ [34, 46]. If the sampling is incomplete, the critical value must be adjusted. Our results were not biased by taxon sampling as indicated by the result of the MCCR test. It is worth noticing that we were very conservative when conducting the MCCR test by adding an extra 10% to the known unsampled diversity.
If the diversification of a group follows a Yule process and the sampling is apparently complete, a bias towards slowdown can still exist if recent lineage splits are unlikely to be considered as distinct species. Indeed, recent lineage splits are likely to be recognized as speciation event only if both lineages persist long enough to evolve differences that attract taxonomic attention . Population-level studies are still scarce in New Caledonia [48–51] but a growing trend has been to include several specimens of the putative same species in phylogenetic reconstruction . In particular, several phylogenies included in the present study have used multiple specimens from the same species that we here considered as separate entities [12, 52, 53] The previous situation is close to the case of non-random sampling where systematists tend to oversample deep nodes to get a better coverage of the taxon's morphological diversity , later referred to as 'diversified sampling' . Studies in New Caledonia are usually performed with the aim of inferring biogeographic evolutionary history rather than simply reconstructing the systematics of the group. In addition, most of our datasets have a relatively low number of missing taxa and in all cases, the proportion of sampled species is more than the 80% level recently proposed as a threshold [54, 56].
A pattern of slowdown in large clades is expected under constant speciation-extinction models, whenever the extinction rate is low . Due to stochasticity, large clades (produced if, by chance, multiple speciation events happened early in the diversification) and small clades (produced if, by chance, few speciation events happened early in the diversification) will both tend to go back to the average speciation rate following a regression effect. Under this situation, we expect to see an apparent slow down in large clades and acceleration in small clades. Our results are not consistent with this situation as the largest diversification (Agmina) shows a relatively low γ while Troglosironidae, with only 11 species, shows one of the highest negative γ.
As explained recently , negative γ can also be achieved if a clade is in significant decline. There are numerous examples from the fossil record showing clades in decline  and recent taxa that have become extinct can only be assessed using the fossil record. Unfortunately, in many cases (especially in New Caledonia), there is no good fossil record and molecular phylogenies cannot infer declines. The average rate of diversification needed to account for the living diversity may have nothing to do with the actual diversity trajectory that led to the living diversity. As for all the studies on diversity dynamics, the absence of information from the extinct species is a severe limitation .
Towards a rejection of the museum model?
The museum model makes the assumption that there is a strong correlation between clade age and species richness. Our results show evidence for diversification slowdown suggesting that diversification might be diversity-dependent. In addition, seven of the nine datasets present are better explained by a diversity-dependent model than alternative models of diversification. This pattern of evolution has long been observed in the fossil record [60–62]. This general model also explains why many studies have shown that clade age and clade size are not related [63–65]. For our studies, there is also an evident decoupling between clade age and clade size (Pearson correlation factor r = 0.22).
Constant birth and extinction rates produce an apparent increase in diversification rates on the reconstructed phylogenies. Under this scenario, we would expect a positive γ . This indicates that our results broadly reject a constant rate diversification process, whether diversifications followed a Pure Birth or a Birth-Death model. However, if clades are too young, we could observe an apparent absence of diversity regulation that results from insufficient time to reach carrying capacity . Recent simulation studies have indeed demonstrated that during the early phase of a logistic growth, the γ statistic is unable to identify a diversity-dependent process .
Our results based on the diversity dynamics of the phylogenies reject the museum model. They also agree with molecular dating results, rejecting the hypothesis that the distribution of New Caledonian groups could be explained by vicariance from Gondwana around 80 Ma . Perhaps the most unusual case is the New Caledonian endemic harvestman family Troglosironidae, sister to the Tropical Gondwanan family Neogovidae . The start of the diversification of the group was estimated at 28-49 MYA in . The age of the same group is currently estimated to be around 77 Ma ('much pre-dating the total submersion episode that would have ended by 37 Ma') but this study only included two species . This group has consistently been presented as a Gondwanan relict whose presence in New Caledonia had to be explained by vicariance  even though confidence intervals [68, 69] are also consistent with a more recent dispersal scenario. Our results indicate that the diversification of Troglosironidae in New Caledonia show the same characteristics as other diversifications (e.g. Niemeyera), suggesting a diversity-dependent process of diversification after recolonization.
Alternative Gondwanan models?
In this paper, we specifically tested a model of biodiversity (the museum model) where species with a Gondwanan origin in New Caledonia would have evolved following an exponential model (implying constant rates of speciation and extinction (if any) in a stable environment). Alternatively, we could imagine additional models where the New Caledonian clades still take their origin from a vicariant event due to the fragmentation of Gondwana.
Under a hypothesis of a constant speciation/extinction rate process (as in the museum model), we could also imagine that an event of mass extinction occurred. This model results in LTT plots showing antisigmoid curves with a distinct signature (a 'broom and handle' shape) . They rise steeply at first, curve to a plateau and rise steeply again to the present. Even though those LTT plots were shown to be indistinguishable from those produced by a model where rates are constant but interrupted by a phase of stasis , they are still very different from those produced by typical diversity-dependent models such as in our results (Figure 2).
Another alternative is where the New Caledonian original stock from Gondwana would have evolved following a diversity-dependent model. What are the expectations of such a model? It was originally suggested that a signature of diversity-dependence could only be observed if extinction was zero . However, further simulation studies demonstrated that substantial extinction can occur without erasing the signal of an underlying decreasing diversification rate provided the initial speciation rate is high enough . It is in fact the ratio between the initial speciation rate and the rate of extinction at equilibrium (the so-called 'LiMe ratio') that is critical in determining the shape of the phylogeny. For low values of LiMe, diversity-dependent diversification produces phylogenies that are indistinguishable from those expected under sustained and constant rates of diversification .
There is strong evidence for an initially high speciation rate in association with ecological opportunity, both in the case of mass extinction  and colonization of recent islands [20, 76]. In the case of an already filled geographical and ecological space, as it is hypothesised in our alternative Gondwanan model, we would expect speciation rates to be relatively low. In this case, the low LiMe value would erase the diversity-dependent signal and we would expect γ values to be non-significant.
Even if we imagine that the LiMe ratio was sufficiently high to produce a pattern of diversity-dependence, another issue remains. Considering that New Caledonia broke off from the Eastern margin of Gondwana a long time ago (around 80 Ma), under a model of diversity-dependence, we would expect most of the clades to have reached their equilibrium and entered a state of species turnover at constant diversity. Recent simulation studies have demonstrated that in the case of a diversity-dependence process with high LiMe ratio, there is only a short temporal window where the γ statistics can detect a diversification slowdown. Shortly after the equilibrium is attained, the average γ becomes indistinguishable from the null model of a constant diversification rate .
Under our alternative Gondwanan scenario, we would expect to observe constant rates of diversification and no apparent slowdown. This is either related to the low LiMe ratio or the fact that clades have long reached their equilibrium. Considering that our results show evidence of slowdown in New Caledonian diversifications, we also reject this alternative model.
Impact of biotic interactions
It was recently argued that 'ancient radiations' or 'repeated dispersals' were two opposing explanations for New Caledonian biodiversity [13, 77]. This simplistic view is however confusing since 'repeated dispersal' represents a pattern while 'ancient radiation' implies a process of diversification. The two elements are thus not necessarily in opposition. Our results indicate that in several cases, evidence of an early burst of diversification (consistent with a radiation process) is observed, even though multiple dispersal events have been inferred.
In the case of Niemeyera , based on pairwise genetic divergence and the slowest rate available, the authors previously concluded  that the oldest divergence between sister Australian and New Caledonian taxa might have taken place approximately 32.4 MA. They also showed that two other groups of Sapotaceae are present on the island. Here, we studied the oldest diversification which diversified substantially. In the case of caddisflies, it seems that the diversification of a young clade (Caledomina) with few species has been impeded by competition with the closely related older Agmina extremely diverse radiation .
An alternative example is given by the case of the diving beetles, Papuadytes. The group is absent from Fiji where the genus Copelatus diversified extensively , partly occupying the same habitats as Papuadytes in New Caledonia. Conversely, Copelatus is absent in New Caledonia suggesting that competition between groups is an important factor in explaining their distribution. In contrast to the Niemeyera example, the older New Caledonian Papuadytes group (c. 14 Ma) has only two species representing relictual species pushed to marginal habitats (high altitudes) by subsequent arrivals (c. 9 Ma) .
These examples clearly highlight the role of interspecific competition, providing further evidence for the finding that diversification processes in New Caledonia follow a diversity-dependent model.
Role of ecology and geography
Early bursts followed by a slowdown in diversification are usually interpreted within a framework of adaptive radiation . However, the notion of adaptive radiation [60, 82] specifically refers to the evolution of ecological and phenotypic diversity within a rapidly multiplying lineage , and thus not just to a pattern of temporal variation in diversification rates. Coarse-grained niche modeling studies have shown that climate variables are broadly similar among related species [83, 84]. However, few examples show that differences in fine-scale micro-habitat exist in groups that are otherwise similar in their climatic requirements [11, 80]. There are very few studies investigating the rate of trait evolution through time [33, 85–88] and none of the New Caledonian studies have addressed this critical issue. It is thus apparent that the adaptive nature of the New Caledonian radiation is far from being established. In a neutral setting, allopatric speciation related to vicariance will result in a split of the ancestral geographical space [89–91]. The newly created restricted ranges will likely influence further diversification rates because speciation and extinction rates are related to the species range . A recent simulation study has shown that slowdown in diversification rates can be related to a purely geographical process .
The reduction of range size related to speciation will, in turn, lower the probability of speciation, leading to a temporal slowdown in diversification rate. Under this scenario, it is the reduced geographical opportunity (rather than the ecological opportunity) that is responsible for the slowdown. It is also worth noting that the elongated shape of the main island of New Caledonia (with a high ratio of the long to the short axis) is likely to influence speciation probabilities because linear distributions are more likely to be bisected by geographic barriers. In this context, radiations would be non-adaptative [94–96] and deciphering the adaptive nature of New Caledonian radiation becomes, once again, a critical issue.
In this paper, we reanalyzed all the molecular datasets for New Caledonia that were suitable for our purposes. We reconstructed the phylogenies using standardized methodology, used two ultrametrization alternatives, and took into account phylogenetic uncertainty as well as incomplete taxon sampling when conducting diversification rate constancy tests. Our results provide evidence that the New Caledonian diversifications follow a process of diversity-dependence. This model is consistent with the geological history that indicates a complete submersion of the territory after its breakup from Gondwana . The island was established around 37 Ma, providing an empty geographical and ecological space facilitating evolutionary radiations.
Despite a growing number of phylogenetic studies investigating patterns and timings of diversifications in New Caledonia, the adaptive or non-adaptive nature of those radiations, including their related phenotypic divergences, remains largely unknown. In addition, the influence of phylogenetic niche conservatism/evolution, both at a large (climatic) and fine (habitat) scale needs to be further evaluated [83, 84]. Our approach could be applied to other continental islands such as New Zealand and Madagascar where similar debates about the origin of their biodiversity have emerged [97, 98].
Our selection of datasets was based on clear criteria. Phylogeography studies were not included as branching patterns do not correspond to speciation events . Phylogenetic analyses had to be based (at least partly) on molecular data. We thus discarded all the published phylogenies only based on morphological data . Species diversification in New Caledonia had to be substantial to be incorporated (at least ten species). We thus discarded all the published phylogenies presenting small diversifications [77, 99], including only few species from New Caledonia [100, 101] or only performed at the genus level . The original dataset had to show phylogenetic resolution among the New Caledonian species. We thus discarded all the published phylogenies with little to no resolution [103–105]. Finally, the dataset had to include all the species (or at least most of the species) of a monophyletic New Caledonian group. We discarded studies [11, 106] that included only part (one genus) of monophyletic groups in New Caledonia  or paraphyletic New Caledonian groups [108, 109]. All the included members could be interpreted as classical Gondwanan groups based solely on their distribution.
The Niemeyera dataset  consists of a monophyletic group (the "Niemeyera complex" of the Sapotaceae subfamily Chrysophylloideae) of 47 species (36 known species with several undescribed species) sister to a group of Australian species. Eight species for which material was unavailable were not included in the study. Three accessions of Pycnandra fastuosa were included in the study. The results were not conclusive regarding the monophyly of the species and the branch lengths were also longer than between member of different species. For these reasons, we kept in our analyses those three accession as separate entities.
The Scincidae dataset  includes 42 species representing all the recognized species of Scincid lizards of New Caledonia except five. The Tasmantis (Zealandia) clade was found monophyletic but not the New Caledonian species. We used in the present study the larger monophyletic diversification in New Caledonia. The two specimens of Nannoscincus gracilis, Caledoniscincus austrocaledonicus and Nannoscincus mariei were kept as separate entities as they do not form a monophyletic group.
The Troglosironidae dataset  consists of a monophyletic group of 11 species of harvestmen (among the 13 species known from New Caledonia) representing the full geographical range of the group. All of the species are endemic and comprised in one endemic genus in one endemic family. The Troglosironidae study  was based on direct optimization  and it was thus necessary to reanalyze the dataset.
For the Papuadytes dataset , the authors concluded that lineages of those diving beetles colonized New Caledonia twice, around 14 and 9 Ma (for the larger diversification), and both lineages are derived from an Australian ancestor. We included 15 species of the larger diversification which is currently estimated at 18 species.
The Gracilipsodes dataset  is a New Caledonian endemic genus of caddisflies (Trichoptera) in the family Leptoceridae. The genus at present consists of 10 species and is sister group to the eastern Australian monotypic genus Triplexa. No dating is available for this dataset.
The Helicopha dataset  is a monophyletic genus of caddisflies in the family Helicophidae with currently 18 described species, of which 17 are included in the dataset in addition to two still undescribed species. Four members of the genus are also found in Australia. No dating is available for this dataset.
The Xanthochorema dataset  is a monophyletic New Caledonian endemic genus (9 described and one undescribed species) of caddisflies with free-living predatory larvae in the family Hydrobiosidae . The sister group Psilochorema is found in New Zealand.
The Hydropsychinae dataset  showed that there was only a single diversification of Hydropsychinae caddisflies in New Caledonia and not three as previously thought. This radiation consists of 27 described species of which 26 are included in the dataset. Additionally three specimens of the species Caledopsyche atalanta and two specimens of Orthopsyche nadauna are included since the branch lengths between these specimens are longer than between different species. The total dataset therefore includes 28 species in total. An age of approximately 28.2 Ma has been estimated for this group .
The Agmina dataset consists of a monophyletic endemic diversification of caddisflies with at least 80 species (only 27 are presently described), of which 75 are included in the phylogeny . This is the largest animal diversification known from New Caledonia. Agmina split off from its Australian ancestor around 36,6 Ma (CI: 29.7-48.3 Ma) ago and the New Caledonian radiation started approximately 21.86 Ma (CI 16.8-24.6 Ma). In the same family (Ecnomidae) there is a second New Caledonian endemic genus (Caledomina) with only 4 known species, which split from its Australian ancestor 25,9 Ma (CI: 21.4-38.2 Ma) and started diversification around 9.5 Ma (CI: 6.4-13.2 Ma). The latter is not included in our analyses.
Phylogenetic inference and dating
Most of the studies previously presented used a variety of alignment and analyses strategies rendering the results difficult to compare or impossible to further analyze. When alignments were not provided by the authors or when Direct Optimization  was previously used, sequences were downloaded from GenBank. All the source phylogenies were reanalyzed for this study. Alignment was performed with MUSCLE 3.6  most accurate algorithm and variable regions were removed using GBLOCK 0.91b  with options -t = d -b5 = h. Concatenation of the genes fragments was performed with PHYUTILITY. When clade ages were not available from the original dataset, we estimated the diversification age (the age of the most common recent ancestor of the group) based on the COI gene with a 2.3% pairwise divergence per million years  calculated with PAUP. It has been shown that this standard Arthropod molecular clock is not always correct , but since age determination was not the main goal of this paper, we included this approach in order to get a rough estimate of the timing of diversification. Pearson's r was calculated to estimate the degree of correlation between clade ages and sizes.
For the maximum likelihood analyses, phylograms were computed using RAxML 7.0.4  with a GTR + Γ model  applied to each partition. Chronograms (i.e. phylogenies with branch length proportional to time) were estimated using standard likelihood methods as implemented in the program R8S 1.71 [124, 125]. We used a cross-validation procedure  to select the best method among those offered by the program. We tested one clock-like method, the Langley and Fitch method , and two relaxed-clock methods, nonparametric rate smoothing  and penalized likelihood . For the penalized likelihood method, the degree of autocorrelation within lineages was estimated using cross-validation, and the smoothing parameter λ defined accordingly. We also tested the performance of two penalty functions, the additive penalty function, which penalizes squared differences in rates across neighboring branches in the tree, and the log penalty function, which penalizes the squared difference in the log of the rates on neighboring branches. A search was then performed using the commands num_time_guesses = 3 (3 initial starting conditions) and check-Gradient in order to validate the results. After pruning the outgroups, all trees were calibrated to a total depth from root to tip of 1.
Bayesian analyses were performed using BEAST 1.5.2  as run on the BIOHPC cluster at Cornell University. We performed two separate runs of 20 million generations with sampling every 1000 generations. For all datasets, the analyses were run under a GTR + Γ model for each partition, using a lognormal relaxed clock. All priors were kept as default except the tree prior which was set to a Yule model and the age of the root of the New Caledonian radiation of interest which we constrained to one using a normal distributed prior with mean 1 and standard deviation of 1× 10-7 (thus roughly corresponding to the calibration used in R8S). Convergence was assessed in TRACER 1.5  and the two runs were thereafter combined in LOGCOMBINER 1.5 in the BEAST package, after removing the First 8000 samples of each run as burn-in. For the Agmina dataset two runs of 40 million generations were performed to ensure convergence.
The linearity for the relationship of log(number of lineages) against time can be visually inspected with a Lineage Through Time plot [131, 132]. If diversification has been constant through time, then a straight line is expected. In addition, the γ test  reduces the information available in a molecular phylogeny to a single number, which provides insight into whether the net rate of diversification decreased over time. The γ statistic describes the center of mass for the nodes in a chronogram. Under a pure birth model, this statistic follows a normal distribution with mean = 0 and standard deviation = 1. For a given phylogeny with no missing taxa, a constant rate of diversification is rejected if γ < −1.645 (type I error probability α = 0.05, one tailed) and nodes are more concentrated towards the base of the clade.
The Lineage Through Time (LTT) plots [131, 132] and γ statistic  were computed with APE. For the chronogram obtained under bayesian analysis, we calculated the γ statistic for the maximum clade probability tree with mean node heights. The γ statistic was calculated for 1000 trees drawn randomly from the posterior distribution to get a measure of uncertainty in our estimates. The γ statistic assumes complete taxon sampling, which is not true (or probably not true) for our phylogenies. Because incomplete taxon sampling could bias the estimates of γ [34, 134], we conducted a Monte Carlo constant rates test as implemented in LASER with 5000 replicates. Phylogenies were simulated to the hypothetical full clade size (known missing taxa + 10% unknown missing taxa) under a constant rate pure birth diversification process and taxa were randomly pruned from the tree to mimic incomplete sampling.
Finally, probabilistic models  were evaluated by maximum likelihood in order to investigate more complex temporal patterns of diversification. Diversification parameters were computed using the best-fitting model among two rate-constant (Yule 1-rate and birth-death model) [131, 136] and three rate-variable diversification models (Yule 2-rate, diversity dependent linear, diversity dependent exponential) . P values were calculated by generating 1000 trees under a Yule model assuming 10% missing taxa in addition to the known non-sampled taxa as indicated in the original article. When decreases in diversification rates are observed, new models can be used for explicitly parsing out the relative importance of changes in speciation and extinction rates [73, 74, 137, 138]. The first model of diversification (SPVAR) is characterized by an exponential diversity-dependent speciation rate and a constant extinction rate [139, 140]. The second model (EXVAR) uses a constant speciation rate and linear diversity-dependent extinction. The third model (BOTHVAR) uses linear diversity-dependence for both speciation and extinction rates . Model fitting was conducted with LASER. Model selection was performed by calculating the difference in the Akaike Information Criterion  score (ΔAIC) between the best rate-constant and the best rate-variable models .
Myers N: Threatened biotas: "Hot spots" in tropical forests. Environmentalist. 1988, 8 (3): 187-208. 10.1007/BF02240252.
Myers N, Mittermeier RA, Mittermeier CG, da Fonseca GA, Kent J: Biodiversity Hotspots for conservation priorities. Nature. 2000, 403 (6772): 853-858. 10.1038/35002501.
Thorne RF: Floristic relationships of New Caledonia. The University of Iowa Studies in Natural History. 1965, 21: 1-14.
Jaffré T: Floristic and ecological diversity of the vegetation on ultramafic rocks in New Caledonia. The Vegetation of Ultramafic (Serpentine) soils. Edited by: Baker AJM, Proctor J, Reeves RD. 1992, Intercept, Andover, 101-107.
Morat P: The terrestrial biota of New Caledonia. Biodiv Lett. 1993, 1: 69-71. 10.2307/2999749.
Kier G, Kreft H, Lee TM, Jetz W, Ibisch W, Nowicji C, Mutke J, Barthlott W: A global assessment of endemism and species richness across island and mainland regions. Proc Natl Acad Sci USA. 2009, 106 (23): 9322-9327. 10.1073/pnas.0810306106.
Lowry II PP: Diversity, endemism, and extinction in the flora of New Caledonia, a review. Proceedings of the International Symposium on Rare, Threatened, and Endangered Floras of Asia and the Pacific Rim. Edited by: Peng CI, Lowry PP II. 1998, Taipei, Taiwan: Academia Sinica, 181-206.
Morat P, Jaffré T, Veillon JM: The flora of New Caledonia's calcareous substrates. Adansonia. 2001, 23: 109-127.
Murienne J: New Caledonia: biology. Encyclopedia of Islands. Edited by: Gillespie RG, Clague D. 2009, Berkeley: University of California Press, 643-645.
Murienne J: Testing biodiversity hypotheses in New Caledonia using phylogenetics. J Biogeogr. 2009, 36: 1433-1434. 10.1111/j.1365-2699.2009.02143.x.
Murienne J, Grandcolas P, Piulachs M, Bellés X, D'Haese C, Legendre F, Pellens R, Guilbert E: Evolution on a shaky piece of Gondwana: is local endemism recent in New Caledonia?. Cladistics. 2005, 21 (1): 2-7. 10.1111/j.1096-0031.2004.00042.x.
Espeland M, Johanson KA: The effect of environmental diversification on species diversification in New Caledonian caddisflies (Trichoptera: Hydropsychidae). J Biogeogr. 2010, 37: 979-890.
Grandcolas P, Murienne J, Robillard T, Desutter-Grandcolas L, Jourdan H, Guilbert E, Deharveng L: New Caledonia: a very old Darwinian island?. Philos Trans R Soc B. 2008, 363 (1508): 3309-3317. 10.1098/rstb.2008.0122.
Stebbins GL: Flowering plants, evolution above the species level. 1974, Cambridge, Massachusetts, USA: Harvard University Press
Gaston KJ, Blackburn TM: The tropics as a museum of biological diversity: an analysis of the New World avifauna. Proc R Soc B. 1996, 263 (1366): 63-68. 10.1098/rspb.1996.0011.
Morat P: Our knowledge of the flora of New Caledonia: endemism and diversity in relation to vegetation types and substrates. Biodiv Lett. 1993, 1: 72-81. 10.2307/2999750.
Benton MJ, Emerson BC: How did life become so diverse? The dynamics of diversification according to the fossil record and molecular phylogenies. Palaeontology. 2007, 50: 23-40. 10.1111/j.1475-4983.2006.00612.x.
Stanley SM: An analysis of the history of marine animal diversity. Paleobiology. 2007, 33 (suppl 4): 1-55.
Pelletier B: Geology of the New Caledonia region and its implications for the study of the New Caledonian biodiversity. Compendium of marines species from New Caledonia, Dossiers Scientifiques et Techniques, II7. Edited by: Payri C, Richer de Forges B. 2006, Nouméa, New Caledonia: IRD, 19-32.
Schluter D: The ecology of adaptive radiation. 2000, New York, N. Y.: Oxford University Press
Yoder JB, Clancey E, Des Roches S, Eastman JM, Gentry L, Godsoe W, Hagey TJ, Kochimsen D, Oswald BP, Robertson J, Sarver BAJ, Schenk JJ, Spear SF, Harmon LJ: Ecological opportunity and the origin of adaptive radiations. J Evolution Biol. 2010, 23: 1581-1596. 10.1111/j.1420-9101.2010.02029.x.
Walker TD, Valentine JW: Equilibrium models of evolutionary species diversity and the number of empty niches. Am Nat. 1984, 124: 887-899. 10.1086/284322.
Valentine JW: Biotic diversity and clade diversity. Phanerozoic diversity patterns. Edited by: Valentine JW. 1985, Princeton, N. J.: Princeton University Press, 419-424.
MacArthur RH, Wilson EO: The theory of island biogeography. 1967, N. J.: Princeton University Press, Princeton
MacArthur RH: Patterns of communities in the tropics. Biol J Linn Soc. 1969, 1: 19-30. 10.1111/j.1095-8312.1969.tb01809.x.
Wilson EO: The species equilibrium. Diversity and stability in ecological systems. Edited by: Woodwell M, Smith HH. 1969, Brookhaven National Laboratory, 38-47.
Raup D: Taxonomic diversity during the Phanerozoic. Science. 1972, 177: 1065-1071. 10.1126/science.177.4054.1065.
Sepkoski J, J J: A kinetic model of Phanerozoic taxomomic diversity I. Analysis of marine orders. Paleobiology. 1978, 4: 223-251.
Sepkoski J, J J: A kinetic model of Phanerozoic taxomomic diversity II. Phanerozoic families and multiple equilibria. Paleobiology. 1979, 5: 222-251.
Sepkoski J, J J: A kinetic model of Phanerozoic taxomomic diversity III. Post-Paleozoic families and mass extinctions. Paleobiology. 1984, 10: 247-267.
McPeek MA: The ecological dynamics of clade diversification and community assembly. Am Nat. 2008, 172 (6): 270-284. 10.1086/593137.
Rabosky DL: Heritability of extinction rates links diversification patterns in molecular phylogenies and fossils. Syst Biol. 2009, 58: 629-640. 10.1093/sysbio/syp069.
Mahler DL, Revell LJ, Glor RE, Losos JB: Ecological opportunity and the rate of morphological evolution in the diversification of Greater Antillean Anoles. Evolution. 2010
Pybus OG, Harvey PH: Testing macro-evolutionary models using incomplete molecular phylogenies. Proc R Soc B. 2000, 267: 2267-2272. 10.1098/rspb.2000.1278.
Rabosky DL: Likelihood methods for detecting temporal shifts in diversification rates. Evolution. 2006, 60 (6): 1152-1164.
Fordyce JA: Interpreting the γ statistic in phylogenetic diversification rate studies: a rate decrease does not necessarily indicate an early burst. PLoS ONE. 2010, 5 (7): e11781-10.1371/journal.pone.0011781. [http://dx.plos.org/10.1371/journal.pone.0011781]
Revell LJ, Harmon LJ, Glor RE: Underparameterized model of sequence evolution leads to bias in the estimation of diversification rates from molecular phylogenies. Syst Biol. 2005, 54 (6): 973-983. 10.1080/10635150500354647.
Barraclough TG, Nee S: Phylogenetics and speciation. Trends Ecol Evol. 2001, 16 (7): 391-399. 10.1016/S0169-5347(01)02161-9.
Gu X, Fu YX, Li WH: Maximum Likelihood estimation of the heterogeneity of substitution rate among nucleotide sites. Mol Biol Evol. 1995, 12 (4): 546-557.
Yang Z: Computational Molecular Evolution. 2006, London: Oxford University Press
Sullivan J, Swofford DL, Naylor GJP: The effect of taxon sampling on estimating rate heterogeneity parameters of Maximum-Likelihood models. Mol Biol Evol. 1999, 16 (10): 1347-1356.
Mayrose I, Friedman N, Pupko T: A Gamma mixture model better accounts for among site rate heterogeneity. Bioinformatics. 2005, 21: 151-158.
Barraclough TG, Vogler AP: Recent diversification rates in North American tiger beetles estimated from a dated mtDNA phylogenetic tree. Mol Biol Evol. 2002, 19: 1706-1716.
Martin AP, Costello EK, Meyer AF, Nemergut DR, Schmidt SK: The rate and pattern of cladogenesis in microbes. Evolution. 2004, 58: 946-955.
Rüber L, Zardoya R: Rapid cladogenesis in marine fishes revisited. Evolution. 2005, 59: 1119-1127.
Pybus OG, Rambaut A, Holmes EC, Harvey PH: New inferences from tree shape: numbers of missing taxa and population growth rates. Syst Biol. 2002, 51: 2267-2272.
Purvis A, Orme CDL, Toomey NH, Pearson PN: Temporal patterns in diversification rates. Speciation and patterns of diversity. Edited by: Butlin R, Bridle JR, Schluter D. 2009, British Ecological Society, Cambridge, U. K.: Cambridge University Press
Bottin L, Verhaegen D, Tassin J, Olivieri I, Vaillant A, Bouver JM: Genetic diversity and population structure of an insular tree, Santalum austrocaledonicum in New Caledonian archipelago. Mol Ecol. 2005, 14: 1979-1989. 10.1111/j.1365-294X.2005.02576.x.
Bottin L, Tassin J, Nasi R, Bouvet JM: Molecular, quantitative and abiotic variables for the delineation of evolutionary significant units: case of sandalwood (Santalum austrocaledonicum Vieillard) in New Caledonia. Conserv Genet. 2007, 8: 99-109.
Kurata K, Jaffré T, Setoguchi H: Genetic diversity and geographical structure of the pitcher plant Nepenthes vieillardii in New Caledonia: a chloroplast DNA haplotype analysis. Am J Bot. 2008, 95 (12): 1632-1644. 10.3732/ajb.0800129.
Murienne J, Edgecombe GD, Giribet G: Comparative phylogeography of the centipedes Cryptops pictus and Cryptops niuensis (Chilopoda) in New Caledonia, Fiji and Vanuatu. Org Divers Evol. 2011, 11: 61-74. 10.1007/s13127-011-0041-7.
Swenson U, Lowry II PP, Munzinger J, Rydin C, Bartish IV: Phylogeny and generic limits in the Niemeyera complex of New Caledonian Sapotaceae: evidence of multiple origins of the anisomerous flower. Mol Phylogenet Evol. 2008, 49: 909-929. 10.1016/j.ympev.2008.09.022.
Smith SA, Sadlier RA, Bauer AM, Austin CC, Jackman T: Molecular phylogeny of the scincid lizards of New Caledonia and adjacent areas: Evidence for a single origin of the endemic skinks of Tasmantis. Mol Phylogenet Evol. 2007, 43: 1151-1166. 10.1016/j.ympev.2007.02.007.
Cusimano N, Renner SS: Slowdowns in diversification rates from real phylogenies may not be real. Syst Biol. 2010, 59 (4): 458-10.1093/sysbio/syq032.
Höhna S, Stadler T, Ronquist F, Britton T: Inferring speciation and extinction rates under different species sampling schemes. Mol Biol Evol. 2011
Morlon H, Potts MD, Plotkin JB: Inferring the dynamics of diversification: a coalescent approach. PLoS Biology. 2010, 8 (9): e1000493-10.1371/journal.pbio.1000493.
Philimore AB, Price TD: Density-dependent cladogenesis in birds. PLoS Biology. 2008, 6 (3): e71-10.1371/journal.pbio.0060071.
Quental TB, Marshall CR: Diversity dynamics: molecular phylogenies need the fossil record. Trends Ecol Evol. 2010, 25: 434-441. 10.1016/j.tree.2010.05.002.
Foote M: Symmetric waxing and waning of marine animal genera. Paleobiology. 2007, 333: 517-529.
Simpson GG: The major features of evolution. 1953, New York, N. Y.: Columbia University Press
Sepkoski J, J J: Rates of speciation in the fossil record. Philos Trans R Soc B. 1998, 353: 315-326. 10.1098/rstb.1998.0212.
Stanley SM: Macroevolution: pattern and process. 1979, San Fransisco, U.S.A.: W. H. Freeman
McPeek MA, Brown JM: Clade age and not diversification rate explains species richness among animal taxa. Am Nat. 2007, 169: E97-E106. 10.1086/512135.
Ricklefs RE: Global variation in the diversificatio rate of passerine birds. Ecology. 2006, 87: 1424-1431. 10.1890/0012-9658(2006)87[1424:TUNTOB]2.0.CO;2.
Ricklefs RE, Losos JB, Townsend TM: Evolutionary diversification of clades of squamate reptiles. J Evolution Biol. 2007, 20: 1751-1762. 10.1111/j.1420-9101.2007.01388.x.
Rabosky DL: Ecological limits and diversification rate: alternative paradims to explain the variation in species richness among clades and regions. Ecol Lett. 2009, 12: 735-743. 10.1111/j.1461-0248.2009.01333.x.
Liow LH, Quental TB, Marshall CR: When can decreasing diversification rates be detected with molecular phylogenies and the fossil record?. Syst Biol. 2010, 59 (6): 646-659. 10.1093/sysbio/syq052.
Boyer SL, Clouse RM, Benavides LR, Sharma P, Schwendinger J, Karunarathna I, Giribet G: Biogeography of the world, a case study from cyphophthalmid Opiliones, a globally distributed group of arachnids. J Biogeogr. 2007, 34 (12): 2070-2085. 10.1111/j.1365-2699.2007.01755.x.
Giribet G, Vogt L, Pérez-González A, Sharma P, Kury AB: A multilocus approach to harvestman (Arachnida: Opiliones) phylogeny with emphasis on biogeography and the systematics of Laniatores. Cladistics. 2010, 26 (4): 408-437.
Sharma P, Giribet G: A relict in New Caledonia: phylogenetic relationships of the family Troglosironidae (Opiliones: Cyphophthalmi). Cladistics. 2009, 25: 1-16. 10.1111/j.1096-0031.2008.00233.x.
Crisp MD, Cook LG: Explosive radiation of cryptic mass extinction? Interpreting signatures in molecular phylogenies. Evolution. 2009, 63 (9): 2257-2265. 10.1111/j.1558-5646.2009.00728.x.
Stadler T: Simulating Trees with a Fixed Number of Extant Species. Syst Biol. 2011
Rabosky DL, Lovette IJ: Explosive evolutionary radiations: decreasing speciation or increasing extingction through time?. Evolution. 2008, 62 (8): 1866-1875. 10.1111/j.1558-5646.2008.00409.x.
Quental TB, Marshall CR: Extinction during evolutionary radiations: reconciling the fossil record with molecular phylogenies. Evolution. 2009, 63 (12): 3158-3167. 10.1111/j.1558-5646.2009.00794.x.
Foote M: The evolution of morphilogical diversity. Annu Rev Ecol Evol Sys. 1997, 28: 129-152. 10.1146/annurev.ecolsys.28.1.129.
Schluter D: Ecology and the origin of species. Trends Ecol Evol. 2001, 16: 372-380. 10.1016/S0169-5347(01)02198-X.
Nattier R, Robillard T, Desutter-Grandcolas L, Couloux A, Grandcolas P: Older than New Caledonia emergence? A molecular phylogenetic study of the eneopterine crickets (Orthoptera: Grylloidea). J Biogeogr. 2011
Bartish IV, Swenson U, Munzinger J, Anderberg AA: Phylogenetic relationships among New Caledonian Sapotaceae (Ericales): molecular evidence for generic polyphyly and repeated dispersal. Am J Bot. 2005, 92 (4): 667-673. 10.3732/ajb.92.4.667.
Espeland M, Johanson KA: The diversity and radiation of the largest monophyletic animal group on New Caledonia (Trichoptera: Ecnomidae: Agmina). J Evolution Biol. 2010, 23: 2112-2122. 10.1111/j.1420-9101.2010.02072.x.
Balke M, Wewalka G, Alarie Y, Ribera I: Molecular phylogeny of Pacific island Colymbetinae: radiation of New Caledonian and Fijian species (Coleoptera, Dytiscidae). Zool Scr. 2007, 36 (2): 173-200. 10.1111/j.1463-6409.2006.00265.x.
Balke M, Pons J, Ribera I, Sagata K, Vogler AP: Infrequent and unidirectional colonization of hyperdiverse Papuadytes diving beetles in New Caledonia and New Guinea. Mol Phylogenet Evol. 2007, 42: 505-516. 10.1016/j.ympev.2006.07.019.
Simpson GG: Tempo and mode in evolution. 1944, New York, N. Y.: Columbia University Press
Murienne J, Pellens R, Grandcolas P: Short-range endemism in New Caledonia. Distribution and new species in the genus Lauraesilpha. Zoologia Neocaledonica 7, Biodiversity Studies. Edited by: Grandcolas P. 2008, 197: 261-271.
Murienne J, Guilbert E, Grandcolas P: Species' diversity in the New Caledonian endemic genera Cephalidiosus and Nobarnus (Insecta: Heteroptera: Tingidae), an approach using phylogeny and species' distribution modelling. Biol J Linn Soc. 2009, 97: 177-184. 10.1111/j.1095-8312.2008.01184.x.
Harmon LJ, Schulte JA, Larson A, Losos JB: Tempo and mode of evolutionary radiation in iguanian lizards. Science. 2003, 301 (5635): 961-10.1126/science.1084786.
Harmon LJ, Melville J, Larson A, Losos JB: The role of geography and ecological opportunity in the diversification of Day Geckos (Phelsuma). Syst Biol. 2008, 57 (4): 562-573. 10.1080/10635150802304779.
Agrawal AA, Fishbein M, Halitschke R, Hastings AP, Rabosky DL, Rasmann S: Evidence for adaptive radiation from a phylogenetic study of plant defenses. Proc Natl Acad Sci USA. 2009, 106 (43): 18067-10.1073/pnas.0904862106.
Harmon LJ, Losos JB, Davies TJ, Gillespie RG, Gittleman JL, Jennings WB, Kozak KH, McPeek MA, Moreno-Roark F, Near TJ, et al: Early bursts of body size and shape evolution are rare in comparative data. Evolution. 2010, 64 (8): 2385-2396.
Barraclough TG, Vogler AP: Detecting the geographical pattern of speciation from species-level phylogenies. Am Nat. 2000, 155 (4): 419-434. 10.1086/303332.
Waldron A: Null Models of Geographic Range Size Evolution Reaffirm Its Heritability. Am Nat. 2007, 170 (2): 221-231. 10.1086/518963. [http://www.jstor.org/stable/10.1086/518963]
Phillimore AB, Orme CDL, Thomas GH, Blackburn TM, Bennett PM, Gaston KJ, Owens IPF: Sympatric Speciation in Birds Is Rare: Insights from Range Data and Simulations. Am Nat. 2008, 171 (5): 646-657. 10.1086/587074. [http://www.jstor.org/stable/10.1086/587074]
Rosenzweig ML: On continental steady states of speces diversity. The ecology and evolution of communities. Edited by: Cody M, Diamond JM. 1975, Cambridge, Massachusetts, USA: Harvard University Press, 124-140.
Pigot AL, Phillimore AB, Owens IPF, Orme CDL: The shape and temporal dynamics of phylogenetic trees arising from geographic speciation. Syst Biol. 2010, 59 (6): 660-673. 10.1093/sysbio/syq058.
Gittenberger E: What about non-adaptive radiation?. Biol J Linn Soc. 1991, 43: 263-272. 10.1111/j.1095-8312.1991.tb00598.x.
Gillespie RG: Encyclopedia of Biodiversity, Academic Press. 2001, 25-44. chap. Adaptive radiation
Rundell RJ, Price TD: Adaptive radiation, nonadaptive radiation, ecological speciation and nonecological speciation. Trends Ecol Evol. 2009
Giribet G, Boyer SL: 'Moa's Ark' or 'Goodbye Gondwana': is the origin of New Zealand's terrestrial invertebrate fauna ancient, recent or both?. Invertebr Syst. 2010, 24: 1-8. 10.1071/IS10009.
Warren BH, Strasberg D, Bruggemann JH, Prys-Jones RP, Thébaud C: Why does the biota of the Madagascar region have such a strong Asiatic flavour?. Cladistics. 2010, 26: 526-538. 10.1111/j.1096-0031.2009.00300.x.
Wagstaff SJ, Dawson MI, Venter S, Munzinger J, Crayn DM, Steane DA, Lemson KL: Origin, Diversification, and Classification of the Australasian Genus Dracophyllum (Richeeae, Ericaceae). Ann Missouri Bot Gard. 2010, 97 (2): 235-258. 10.3417/2008130. [http://www.bioone.org/doi/abs/10.3417/2008130]
Page TJ, Baker AM, Cook BD, Hughes JM: Historical transoceanic dispersal of a freshwater shrimp: the colonization of the South Pacific by the genus Paratya (Atyidae). J Biogeogr. 2005, 32: 581-593. 10.1111/j.1365-2699.2004.01226.x.
Harbaugh DT, Baldwin BG: Phylogeny and biogeography of the sandalwoods (Santalum, Santalaceae): repeated dispersals throughout the Pacific. Am J Bot. 2007, 94 (6): 1028-1040. 10.3732/ajb.94.6.1028.
Barker NP, Weston PH, Rutschmann F, Sauquet H: Molecular dating of the 'Gondwanan' plant family Proteaceae is only partially congruent with the timing of the break-up of Gondwana. J Biogeogr. 2007, 34: 2012-2027. 10.1111/j.1365-2699.2007.01749.x.
Setoguchi H, Asakawa Osawa T, Pintaud JC, Jaffire T, Veillon JM: Phylogenetic relationships within Araucariaceae based on rbcL gene sequences. Am J Bot. 1998, 92 (2): 316-329.
Swenson U, Munzinger J, Bartish IV: Molecular phylogeny of Planchonella (Sapotaceae) and eight new species from New Caledonia. Taxon. 2007, 56 (2): 329-354.
Duangjai S, Samuel R, Munzinger J, Forest F, Wallnofer B, Barfuss MHJ, Fischer G, Chase MW: A multi-locus plastid phylogenetic analysis of the pantropical genus Diospyros (Ebenaceae), with an emphasis on the radiation and biogeographic origins of the New Caledonian endemic species. Mol Phylogenet Evol. 2009, 52: 602-620. 10.1016/j.ympev.2009.04.021.
Murienne J, Pellens R, Budinoff RB, Wheeler WC, Grandcolas P: Phylogenetic analysis of the endemic New Caledonian cockroach Lauraesilpha. Testing competing hypotheses of diversification. Cladistics. 2008, 24: 802-812. 10.1111/j.1096-0031.2008.00204.x.
Murienne J: Molecular data confirm family status of the Tryonicus-Lauraesilpha group (Insecta, Blattodea, Tryonicidae). Org Divers Evol. 2009, 9: 44-51. 10.1016/j.ode.2008.10.005.
Buckley TR, Attanayake D, Bradler S: Extreme convergence in stick insect evolution: phylogenetic placement of the Lord Howe Island tree lobster. Proc. R. Soc. B. 2009, 276: 1055-1062. 10.1098/rspb.2008.1552.
Buckley TR, Attanayake D, Nylander JA, Bradler S: The phylogenetic placement and biogeographical origins of the New Zealand stick insects (Phasmatodea). Syst Entomol. 2010, 35 (2): 207-225. 10.1111/j.1365-3113.2009.00505.x.
Wheeler W, Aagesen L, Arango C, Faivovich J, Grant T, D'Haese C, Janies D, Smith L, Varón A, Giribet G: Dynamic homology and phylogenetic systematics: a unified approach using POY. 2006, American Museum of Natural History
Malm T, Johanson KA: Revision of the New Caledonian endemic genus Gracilipsodes (Trichoptera: Leptoceridae: Grumichellini). Zool J Linn Soc Lond. 2008, 153: 425-452. 10.1111/j.1096-3642.2008.00403.x.
Johanson KA, Keijsner M: Phylogeny of the Helicophidae (Trichoptera), with emphasis on the New Caledonian species of Helicopha. Syst Entomol. 2008, 33: 451-483. 10.1111/j.1365-3113.2008.00423.x.
Espeland M, Johanson KA, Hovmöller R: Early Xanthochorema (Trichoptera, Insecta) radiations in New Caledonia originated on ultrabasic rocks. Mol Phylogenet Evol. 2008, 48: 904-917. 10.1016/j.ympev.2008.06.006.
Espeland M, Johanson KA: New species and descriptions of females of the New Caledonian endemic genus Xanthochorema (Trichoptera, Hydrobiosidae). Zoologia Neocaledonica 6. Biodiversity studies in New Caledonia. Edited by: Grandcolas P. 2008, Memoires Memoirs du Museum d'Histoire Naturelle, 197: 79-97.
Wheeler WC: Optimization alignment: The end of multiple sequence alignment in phylogenetics?. Cladistics. 1996, 12: 1-9. 10.1111/j.1096-0031.1996.tb00189.x.
Edgar RC: MUSCLE: A multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004, 32 (5): 1792-1797. 10.1093/nar/gkh340.
Castresana J: Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol. 2000, 17 (4): 540-552.
Smith SA, Dunn CW: Phyutility: a phyloinformatics tool for trees, alignments, and molecular data. Bioinformatics. 2008, 24 (5): 715-716. 10.1093/bioinformatics/btm619.
Brower AVZ: Rapid morphological radiation and convergence among races of the butterfly Heliconius erato inferred from patterns of mitochondrial DNA evolution. Proc Natl Acad Sci USA. 1994, 91: 6491-6495. 10.1073/pnas.91.14.6491.
Swofford DL: PAUP*: Phylogenetic analysis using parsimony (* and other methods), version 4.0b 10. Sinauer Associates, Sunderland, Massachusetts. 2003
Papadopoulou A, Anastasiou I, Vogler AP: Revisiting the insect mitochondrial molecular clock: The Mid-Aegean trench calibration. Mol Biol Evol. 2010, 27: 1659-1672. 10.1093/molbev/msq051.
Stamatakis A: RAxML-VI-HPC: Maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics. 2006, 22 (21): 2688-2690. 10.1093/bioinformatics/btl446.
Yang Z: Maximum-likelihood estimation of phylogeny from DNA sequences when substitution rates differ over sites. Mol Biol Evol. 1993, 10 (6): 1396-1401.
Sanderson MJ: r8s: Inferring absolute rates of molecular evolution and divergence dates in the absence of a molecular clock. Bioinformatics. 2003, 19: 301-302. 10.1093/bioinformatics/19.2.301.
Sanderson MJ: r8s version 1.71. 2006, [Program and documentation available at http://loco.biosci.arizona.edu/r8s/]
Sanderson MJ: Estimating absolute rates of molecular evolution and divergence times: a penalized likelihood approach. Mol Biol Evol. 2002, 19: 101-109.
Langley CH, fitch W: An estimation of the constancy of the rate of molecular evolution. J Mol Evol. 1974, 3: 161-177. 10.1007/BF01797451.
Sanderson MJ: A nonparametric approach to estimating divergence times in the absence of rate constancy. Mol Biol Evol. 1997, 14 (12): 1218-1231.
Drummond AJ, Rambaut A: BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol Biol. 2007, 7 (214):
Rambaut A, Drummond AJ: Tracer v1.5. 2007, [http://beast.bio.ed.ac.uk/Tracer]
Nee S, Mooers AO, Harvey PH: Tempo and mode of evolution revealed from molecular phylogenies. Proc Natl Acad Sci USA. 1992, 89: 8322-8326. 10.1073/pnas.89.17.8322.
Harvey PH, May RM, Nee S: Phylogenies without fossils. Evolution. 1994, 48: 523-529. 10.2307/2410466.
Paradis E, Claude J, Strimmer K: APE: Analyses of phylogenetics and evolution in R language. Bioinformatics. 2004, 20: 289-290. 10.1093/bioinformatics/btg412.
Nee S, Holmes EC, May RM, Harvey PH: Extinction rates can be estimated from molecular phylogenies. Philos Trans R Soc B. 1994, 344: 77-82. 10.1098/rstb.1994.0054.
Kendall DG: On the generalized "birth-and-death" process. Ann Math Stat. 1948, 19: 1-15. 10.1214/aoms/1177730285.
Nee S: Birth-Death models in macroevolution. Annu Rev Ecol Evol Sys. 2006, 37: 1-17. 10.1146/annurev.ecolsys.37.091305.110035.
Bokma F: Problems detecting density-dependent diversification on phylogenies. Proc R Soc B. 2008, 276: 993-994.
Rabosky DL, Lovette IJ: Problems detecting density-dependent diversification on phylogenies: reply to Bokma. Proc R Soc B. 2009, 276: 995-997. 10.1098/rspb.2008.1584.
Alroy J: Constant extinction, constrained diversification, and uncoordinated stasis in North American mammals. Palaeogeogr Palaeocl Palaeoecol. 1996, 127: 285-311. 10.1016/S0031-0182(96)00100-9.
Alroy J: Equilibrial diversity dynamics in North American mammals. Biodiversity dynamics: turnover of populations, taxa and communities. Edited by: McKinney ML, Drake J. 1998, Columbia University Press, New York, NY, 232-287.
Rabosky DL: LASER, a maximum likelihood toolkit for detecting temporal shifts in diversification rates from molecular phylogenies. Evol Bioinform Online. 2006, 2: 247-250.
Akaike H: Information theory and an extension of the maximum likelihood principle. Proceedings of the international symposium on information theory. 1973, Budapest: Akademiai Kiado, 267-281.
We thank M. Balke, U. Swenson, K. A. Johanson, T. Malm and P. Sharma for providing their datasets. We thank T. Quental, N. Wahlberg, A. Antonelli, D. Dimitrov, A. Whibley, the associate editor and two anonymous reviewers for improving the quality of the manuscript. D. Rabosky kindly helped with Laser. J. M. was supported by a Marie Curie International Outgoing Fellowship (grant 221099) within the 7th European Community Framework Program. M.E was supported by the Swedish Research Council (Grant No. 2005-4834 to K. A. Johanson) and the Ebba and René Malaise Foundation. We thank our colleagues of the Institut de Recherche pour le Développement, Direction du Développement Economique et de l'Environnement (Province Nord) and Direction de l'Environnement (Province Sud) for logistical and administrative support during our fieldwork in New Caledonia.
Both authors equally contributed to the study. JM performed the maximum likelihood analyses. ME performed the bayesian analyses. Both authors read and approved the final manuscript.
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Espeland, M., Murienne, J. Diversity dynamics in New Caledonia: towards the end of the museum model?. BMC Evol Biol 11, 254 (2011). https://doi.org/10.1186/1471-2148-11-254
- Extinction Rate
- Diversification Rate
- Ecological Space
- Ecological Opportunity
- Diving Beetle