Here, we show strong support that contemporary hybridization is correlated with elevated diversification rates in the order Caudata. Net-diversification of hybridizing species tends to be significantly greater than that of non-hybridizing species, driven primarily by a coincident increase in speciation and decrease in extinction rates (Figs. 2, 3; Tables 1, 2). The accelerated diversification of hybridizing salamanders appears ephemeral, however; rate differences rapidly become less pronounced deeper in the tree due to turnover of the hidden states (Fig. 1, Supplementary Figs. S9-S12). Possible mechanisms leading to this result include frequent range expansions and contractions (i.e.68) that have been documented in salamanders (e.g.69,70,71) and the process of reinforcement which has long been recognized to contribute to the diversification process14,72,73,74. We outline the potential contribution of each below.

Salamanders often exhibit substantial genetic differentiation at small geographic distances (e.g., 200 m75) owing to limited dispersal abilities and low rates of gene flow76, thus leading to an abundance of opportunities to evolve in allopatry. Additionally, terrestrial species such as the Plethodontid salamanders of the southeastern United States experience elevational range expansions and contractions associated with climatic change71. Perhaps this combination of the primarily sessile nature of many salamander species and frequent repeated secondary contact leads to hybridization occurring regularly across evolutionary timescales. Under these scenarios, hybridization may then play a creative evolutionary role in the diversification process similar to that observed in haplochromine cichlids24,25,77. Allopatric speciation of haplochromine cichlids has occurred in lakes that frequently have dried, split, and reformed, whereas sympatric speciation has occurred within lakes in which lineages exhibited extreme habitat specificity and have been reproductive isolated at fine spatial scales78. Under these circumstances, hybridization may have afforded genetic rescue from the consequences of small population size by providing increased standing genetic variation and thus expedited adaptation to novel stressors, as in Lake Victorian cichlids post-colonization25.

Such hypotheses of repeated contractions, expansions, and secondary contact of salamander populations have been well supported, across both North79,80,81 and South America50,82, as well as in Europe83,84,85. Often associated with glaciation/deglaciation or orogeny of mountain ranges, geological events may act as species pumps for salamanders (i.e.86). However, while periodic geographic range expansion and contraction may initiate speciation, the reproductive isolation that evolves may be incomplete, predisposing the young species/diverging lineages to hybridization (i.e.23). As a result, hybridization may commonly occur in salamanders during periods of climatic fluctuations.

There is now clear evidence for latitudinal and elevational range shifts mediated by climate change87,88,89,90,91 and a consequent increase in frequency of hybridization among previously isolated taxa92,93,94,95. An informed understanding of the influence of hybridization on macroevolutionary diversification may thus provide invaluable context for contemporary processes. This possibility of climate-change mediated hybridization has already been demonstrated in plethodontid salamanders (P. shermani & P. teyahalee71), as well as in ecologically divergent subspecies of salamandrid salamanders (S. salamandra96). Thus, it seems likely that salamander species worldwide, particularly those found at high elevations due to their more limited potential geographic distributions, may experience a heightened frequency of hybridization as climate change advances. While generalizations regarding the outcome of hybridization should be made with caution30, our study indicates that perhaps speciation reversal97,98,99 need not be the expectation. Rather, our study implies that hybridization may facilitate adaptation to novel conditions under climate change, leading to diversification of new salamander lineages.

Here, we show the novel result of a strong correlation of contemporary hybridization with elevated speciation and net diversification at a large taxonomic scale. However, reinforcement, defined as the strengthening of prezygotic reproductive isolation in sympatry14, is intrinsically intertwined with hybridization. Reinforcement has been documented both experimentally72 and observationally74 to accelerate the initiation and/or completion of the speciation process73,100,101. For instance, reinforcement is likely to play an important role in the speciation process due to strong interspecific sexual selection and mate choice in plethodontids102. Indeed, patterns of sexual isolation among populations of Plethodon jordani and P. teyahalee match expectations of reinforcement14, with sexual selection being stronger in sympatry than in allopatry103. Although we cannot currently quantify the contribution of reinforcement to diversification rate differences using our data, we urge further research measuring the degree of association between contemporaneous hybridization and reinforcement among taxa. Nonetheless, were reinforcement to play a role in the production of the patterns observed in this study, the very occurrence/process of hybridization would be the ultimate driver (i.e., cannot have reinforcement without hybridization). Under such a scenario, our study design is well-suited to identify such a signal.

Although a generative role of hybridization is robustly supported across three of our four datasets, evidence for such a role outside of the Plethodontidae is more limited (Table 1, Supplementary Tables S2-S14). We find two possible explanations for this finding. Firstly, the positive association between diversification rates and hybridization may be unique to Plethodontid salamanders. However, family Plethodontidae is the largest extant family of salamanders, comprising approximately 2/3rds of the present diversity (471 of 716 species: amphibiaweb.org). Thus, our observation of hybridization facilitating the diversification process applies to the majority of salamanders and implies that, at a minimum, contemporaneous hybridization does not impede the diversification process of extant salamanders.

Secondly, it is highly probable that our analysis of non-plethodontid salamanders is lacking in power. SSE models have long been known to lose much of their power when dealing with small number of OTUs (trees < 300 taxa104). For example, for trees of 300 species, BiSSE attains a power of at most 50%, with power dropping below 15% of trees of 100 taxa104. Our phylogeny of non-plethodontids includes only 167 species; that we detected a positive relationship between hybridization and speciation rates using our narrow (most conservative) dataset despite such reduced power is a testament to the strength of the signal in our data. Whereas our larger datasets [complete (469 spp), sympatric (368 spp) and plethodontids (306 spp)] have greater power, our lack of detection of a relationship between hybridization and diversification rates in non-plethodontids using our broad definition of hybridization is perhaps unsurprising, given the low power of the analysis (also see Supplementary Materials for an elaboration of power). Although the power of HiSSE under such scenarios has not been specifically established, accuracy of parameter estimation does decay with decreasing tree size61. Consequently, we cautiously interpret the results of the analysis of non-plethodontids (163 spp). Interestingly, sister clade comparisons consistently supported a positive relationship between hybridization and species richness in non-plethodontids, despite not supporting such a relationship in plethodontids (Supplementary Table S16). These results are insensitive to branch-lengths, thereby ameliorating potential concerns related to the relationship between hybridization, branch-lengths, and diversification rates23.

Importantly, parameter estimates are largely reasonable. For instance, the greatest speciation rate inferred by any analysis (Plethodontids assuming 30% of taxa hybridize using the full tree: Supplementary Table S13), of 0.159 species/million years (MY) can be interpreted as a waiting time, such that on average, hybridizing species speciate every 6.29 MY. Extinction rates appear less reliably estimated however; some estimates functionally equal zero, leading to the large percent decrease in extinction rates observed for hybridizing relative to non-hybridizing species. In some cases, extinction rates exceed speciation rates in non-hybridizing taxa, leading to negative net-diversification rates. That being said, averaged extinction rates across all analyses for hybridizing and non-hybridizing taxa led to more reasonable waiting times of 127.9 and 54.2 MY respectively. Further, recent studies have documented even more negative net-diversification rates than inferred herein105. Taken together, it appears that extinction plays an important role in the diversification of salamanders, leading to a reduction in net-diversification rates towards the present relative to hybridizing species.

An important question regarding the interpretation of our results is the relationship between lineage diversification rates, species richness, and opportunity to hybridize. Because the relationship between lineage diversification rate and opportunity to hybridize are not necessarily independent, rapidly diversifying lineages may simply have greater opportunity to hybridize due to increased diversification rates. Although a legitimate concern, we did not find evidence that the increased diversification rates we observe are due to increased family-level species richness leading to increased opportunity to hybridize (Supplementary Fig. S8). Further, it is unlikely that non-random taxonomic sampling has biased our results, as there is no relationship between clade specific sampling fraction and frequency of hybridization (Supplementary Fig. S5).

Although the ability of methods to accurately infer extinction rates has been debated recently63,106,107, we emphasize that our results are robust to this concern. Our central result, that hybridizing lineages experience increased net diversification, is driven by both increased speciation rates and decreased extinction rates. Further, in nearly all cases, the magnitude of increase of speciation rate is greater than that of the decrease in extinction. Thus, our results are likely robust even to inaccuracies in the estimation of extinction rate.

An important distinction between our study and most previous studies investigating the influence that hybridization exerts on the diversification process is that of the time-scale at which hybridization is being assessed. Following Seehausen’s6 landmark paper “Hybridization and Adaptive Radiation,” tests and discussion of his hypothesis, that ancient, widespread hybridization facilitates adaptive radiation became abundant in the literature (e.g.18,22,23,108,109). Whereas much of the subsequent studies focused on ancient hybridization, our study instead focuses on the effects of contemporary hybridization.

In a pertinent study, Wiens et al.23, tested the hybrid swarm hypothesis in the Plethodon glutinosus group (indicated in Fig. 1B) using two nuclear and two mitochondrial genes. They did not recover strongly supported evidence of genealogical discordance at the base of this group; these results were interpreted as not being supportive of Seehausen’s hypothesis. Further, they identified a positive relationship between age of species and reproductive isolation. They argue that the observed relationship between diversification rate and hybridization in this group was a consequence of this relationship. Although a legitimate concern, we argue that this hybridization is likely to still have biologically relevant consequences on diversification rates. Specifically, hybridization may either 1) facilitate the divergence of these young species i.e. through reinforcement/strengthening of prezygotic isolation, or 2) erode their divergence leading to species collapse. Whereas the former hypothesis predicts increased speciation rates, the latter predicts increased extinction rates. We find strong, consistent evidence in favor of the former.

We explicitly tested the hypothesis that contemporary hybridization plays a creative role in the diversification process in the broadest taxonomic and temporal scale study to date, and our observations strongly supported the predictions of this hypothesis. Specifically, hybridization was found to be correlated with both increased speciation rates and decreased extinction rates, resulting in increased net diversification rates relative to non-hybridizing lineages. Although other factors certainly contribute to the observed diversification dynamics, we have shown that hybridization plays a significant role, while accounting for hidden, correlated states in our analysis. Nearly all studies of hybridization have focused on individual case studies in which hybridization results in species collapse98 or promotes diversification in a single species group12,13,22,27. Such studies are necessarily limited in the extent to which their results may be generalized30, particularly because results were equivocal across studies. Consequently, we advocate that our approach can be applied at broad taxonomic and evolutionary timescales to facilitate robust tests of the role of hybridization in the lineage diversification process. We anticipate our results are broadly generalizable to animal groups in which homoploid hybridization occurs because only 17 species of salamanders are known to be polyploid110, and our dataset includes only seven (Ambystoma mexicanum, A. barbouri, A. jeffersonium, A. laterale, A. texanum, A. tigrinum, and Lissotriton vulgaris) hybridizing polyploid taxa (none of which are plethodontids). Our study adds to the growing evidence that hybridization may fuel rapid diversification (e.g.52) and is a compliment to speciation genomics studies characterizing the genomic basis of this process (e.g.17,111). Herein we have shown that hybridization may act as a generative force across a phylogenetic order, and additional studies at such macroevolutionary scales are needed to determine if this pattern holds more generally across the tree of life.