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Ecomorphological diversification following continental colonization in muroid rodents (Rodentia: Muroidea)
Abstract
The emergence of exceptionally diverse clades is often attributed to ecological opportunity. For example, the exceptional diversity in the most diverse superfamily of mammals, muroid rodents, has been explained in terms of multiple independent adaptive radiations. If multiple ecological opportunity events are responsible for generating muroid diversity, we expect to find evidence of these lineages ecologically diversifying following dispersal into new biogeographical areas. In the present study, we tested the trait-based predictions of ecological opportunity using data on body size, appendages, and elevation in combination with previously published data on biogeographical transitions and a time-calibrated molecular phylogeny. We identified weak to no support of early ecological diversification following the initial colonizations of all continental regions, based on multiple tests, including node height tests, disparity through time plots, evolutionary model comparison, and Bayesian analysis of macroevolutionary mixtures. Clades identified with increased diversification rates, not associated with geographical transitions, also did not show patterns of phenotypic divergence predicted by ecological opportunity, which suggests that phylogenetic diversity and phenotypic disparity may be decoupled in muroids. These results indicate that shifts in diversification rates and biogeographically-mediated ecological opportunity are poor predictors of phenotypic diversity patterns in muroids.
Supplementary resource (1)
... Muroid rodents, comprising rats, mice, hamsters, and allies, encompass approximately 26% of all mammalian species and compose a large fraction of mammalian diversity of all continents, except for Antarctica and New Zealand (Burgin et al., 2018(Burgin et al., , 2020Musser & Carleton, 2005). It is estimated that they first appeared in the Eocene in Eurasia (Fabre et al., 2012;Jansa et al., 2009;Musser & Carleton, 2005;Steppan & Schenk, 2017) and, since then, dispersed and colonized the main landmasses on the planet (Alhajeri et al., 2016;McKenna & Bell, 1997;Musser & Carleton, 2005). In South America, muroid rodents are represented primarily by the cricetid subfamily Sigmodontinae, composed mainly by the Oryzomyalia, a subclade encompassing about 93% of the sigmodontine species, excluding only those of the tribes Sigmodontini and Ichthiomyini (Pardiñas et al., 2017;Patton et al., 2015). ...
... This model postulates that explosive speciation follows the access by an ancestral lineage to diverse and abundant resources, prompting the rapid emergence of morphological, physiological, or behavioral specializations, and thus allowing wide exploitation of available resources while reducing competition (Pincheira-Donoso et al., 2015;Stroud & Losos, 2016;Yoder et al., 2010). In addition, EO model predicts that, over time, niches become saturated, resulting in deceleration of rates of speciation and phenotypic evolution (Alhajeri et al., 2016). A recent phylogenetic analysis has found an explosive acceleration in diversification after the Oryzomyalia origin, endorsing expectation of EO (Parada et al., 2015). ...
... In view of this, it has been pointed out that the diversification of alimentary habits, which most directly affects cranio-mandibular morphology, may have not been a key factor for the explosive diversification of sigmodontines in South America (Missagia & Perini, 2018;Pardiñas et al., 2021), and the diversification of locomotor niches, may have played a more relevant role (Maestri et al., 2017). Even so, phenotypic characters of the external morphology, which are supposedly more related to locomotor habits, also did not show evidence of explosive diversification followed by a slowdown in the rate of evolution (Alhajeri et al., 2016). ...
Sigmodontine rodents colonized South America in Late Miocene or earlier, leading to the clade Oryzomyalia, which rapidly radiated in distinct lineages and occupied almost all continental habitats, in a pattern classically interpreted as an adaptive radiation. Nevertheless, no evidence of strong influence of niche diversification on the evolution of cranial and mandibular morphology, or of deceleration in rates of phenotypic evolution in these structures over time following niche saturation, as expected according to the Ecological Opportunity model, has been detected. Here, we investigated morphometric variation among 59 oryzomyalian species using phylogenetically informed comparative analyses for testing (1) if the diversification of locomotor habits played an important role in shaping the morphology of the appendicular skeleton, and (2) if the disparification of appendicular skeleton showed high rates at the early diversification of Oryzomyalia and then has deaccelerated. Results showed that the different locomotor habits are associated with different shapes in both the forelimb and hindlimb, and selection of evolutionary models suggested that each locomotor habit was associated with their own adaptive optima. Moreover, the most extreme and specialized phenotypes, found in the semifossorial species Geoxus valdivianus, Blarinomys breviceps, and Paynomys macronyx, seem to have appeared after events of acceleration in the rates of morphological evolution. On the other hand, no evidence of a reduction in the rate of evolution over time was detected. The results suggest that the acquisition of different locomotor habits in oryzomyalians was associated with morphological specializations in the appendicular skeleton guided by natural selection and that, especially in the case of the evolution of fossoriality, there was a marked change in evolutionary regimes, generating highly modified phenotypes after acceleration of the pace of morphological changes. Despite the strong association between diversification of locomotor niches and evolution of the appendicular skeleton, the diversification of oryzomyalians does not seem to have experienced niche saturation, as noted in some other adaptive radiation events on Neotropics.
... et al. 2012). For example, Schenk et al. (2013) and Alhajeri et al. (2016) used muroid rodents to test whether secondary colonists of continental systems experienced lower diversification rates and limited rates of ecological morphological evolution, respectively. These studies, in sum, recovered little support for decelerating rates of evolution in most systems, suggesting that the ecological opportunity model poorly explains the mode of evolution in Muroidea. ...
... Previous work among muroid rodents corroborates our results of tempo and mode of mandibular evolution. Alhajeri et al. (2016) tested whether muroid rodents exhibited EB evolution consistent with declining ecological opportunity following continental colonization in a suite of ecologically important morphological characters. From a different perspective, Rowe et al. (2016) documented the remarkable convergence among independently evolving carnivorous rodents that exhibit shrewlike morphology (such as Soricomys and Archboldomys on Luzon, and Melasmothrix on Sulawesi) as well as the bizarre "tweezer-snouted" morphology exhibited by Rhynchomys on Luzon and Paucidentomys on Sulawesi (Rowe et al. 2016). ...
... From a different perspective, Rowe et al. (2016) documented the remarkable convergence among independently evolving carnivorous rodents that exhibit shrewlike morphology (such as Soricomys and Archboldomys on Luzon, and Melasmothrix on Sulawesi) as well as the bizarre "tweezer-snouted" morphology exhibited by Rhynchomys on Luzon and Paucidentomys on Sulawesi (Rowe et al. 2016). Both Alhajeri et al. (2016) and Rowe et al. (2016) came to similar conclusions as we did: the classical model of early-burst evolution used to support a hypothesis of adaptive radiation is not the likely mechanism of morphological evolution in muroids broadly, murines specifically, nor even LOE rodents locally. Instead, a constant background process with some major shifts to new adaptive zones appears to provide a better explanation of the observed morphological variation, with similar selective pressures in convergently evolved carnivorous rodents (Table 1, Fig. 2, Table S4). ...
Existing radiations in a spatially‐limited system such as an oceanic island may limit the ecological opportunity experienced by later colonists, resulting in lower macroevolutionary rates for secondary radiations. Additionally, potential colonists may be competitively excluded by these incumbent (resident) species, unless they are biologically distinct (biotic filtering). The extant phenotypic diversity of secondary colonists may thus be impacted by lower rates of phenotypic evolution, exclusion from certain phenotypes, and transitions to new morphotypes to escape competition from incumbent lineages. We used geometric morphometric methods to test whether the rates and patterns of mandibular evolution of the Luzon “Old Endemic” rodent clades, Phloeomyini and Chrotomyini, are consistent with these predictions. Each clade occupied nearly completely separate shape space and partially separate size space. We detected limited support for decelerating and clade‐specific evolutionary rates for both shape and size, with strong evidence for a shift in evolutionary mode within Chrotomyini. Our results suggest that decelerating phenotypic evolutionary rates are not a necessary result of incumbency interactions; rather, incumbency effects may be more likely to determine which clades can become established in the system. Non‐incumbent clades that pass a biotic filter can potentially exhibit relatively unfettered evolution.
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... However, the main cause of uneven diversification patterns in muroids remains elusive. Shifts in muroid diversification rates (rates at which new species form) are not satisfactorily explained by ecological opportunity mediated by biogeographic transitions (Schenk et al. 2013;Alhajeri et al. 2016) nor by trait evolution (diet, habitat, body mass, and relative tail length, Alhajeri and Steppan 2018). In both Alhajeri et al. (2016) and Alhajeri and Steppan (2018), the association between diversity and disparity/evolutionary rate is implied but not directly tested. ...
... Shifts in muroid diversification rates (rates at which new species form) are not satisfactorily explained by ecological opportunity mediated by biogeographic transitions (Schenk et al. 2013;Alhajeri et al. 2016) nor by trait evolution (diet, habitat, body mass, and relative tail length, Alhajeri and Steppan 2018). In both Alhajeri et al. (2016) and Alhajeri and Steppan (2018), the association between diversity and disparity/evolutionary rate is implied but not directly tested. We explicitly examine this association in the present study, by testing the correlation between diversity indices (log richness and diversification rate) with disparity and evolutionary rate . ...
... Variation in both diversity and disparity/evolutionary rate could be explained by other factors such as ecological opportunity mediated by biogeographic transitions. There is some evidence for this presented by Schenk et al. (2013) and Alhajeri et al. (2016), where the primary colonization of South America, Sahul, and Southeast Asia were associated with increased phylogenetic and phenotypic diversification in muroid rodents, although this pattern cannot be generalized to other primary and secondary colonization. Other unexamined triggers of ecological opportunity may also explain patterns of diversity and disparity/evolutionary rate in muroids such as mass extinctions of protagonists and the evolution of key innovations (Simpson 1953;Schluter 2000;Grant and Grant 2008). ...
A positive correlation between diversity and disparity/evolutionary rate is predicted by multiple evolutionary theories. However, recent empirical studies in various taxa do not always find such an association. Similarly, we find no correlation between these two levels of variation, based on cranial morphometric data and molecular phylogenetic data from 317 muroid rodent species and dipodoid outgroups, analyzed using three-dimensional geometric morphometrics. This disassociation was found using both phylogenetic and non-phylogenetic approaches, indicating that an increase in clade richness is not necessarily followed by an increase in morphological divergence and vice versa. Furthermore, the distribution of muroid families in morphospace is highly overlapping suggesting greater variation within than between clades. Taken together with the observation that families with the most distinctive cranial morphologies (nesomyids, dipodids, and spalacids) are the least diverse, indicates that evolution of new cranial morphologies may not play an important role in the diversification of muroid rodents.
... The influence of geography on lineage diversification, particularly the role of ecological opportunity mediated by biogeographic transitions, have been investigated in various taxa [e.g. plants (Hagen and Kadereit 2003;Moore and Donoghue 2007); lizards Pinto et al. 2008); snails (Parent and Crespi 2009); fish (Langerhans 2010); rodents (Schenk et al. 2013;Parada et al. 2015;Alhajeri et al. 2016); ants (Price et al. 2014a); mammals (Rolland et al. 2014); primates (Tran 2014)]. In muroids, with the exception of the primary colonization of South America, biogeographic transitions between continents do not seem to greatly influence diversification rates (Schenk et al. 2013;Alhajeri et al. 2016). ...
... plants (Hagen and Kadereit 2003;Moore and Donoghue 2007); lizards Pinto et al. 2008); snails (Parent and Crespi 2009); fish (Langerhans 2010); rodents (Schenk et al. 2013;Parada et al. 2015;Alhajeri et al. 2016); ants (Price et al. 2014a); mammals (Rolland et al. 2014); primates (Tran 2014)]. In muroids, with the exception of the primary colonization of South America, biogeographic transitions between continents do not seem to greatly influence diversification rates (Schenk et al. 2013;Alhajeri et al. 2016). ...
... In addition to diet and habitat, size (log-transformed adult body mass in grams) and relative tail length (ratio of head-body length to tail length, both in millimeters) were extracted from Alhajeri et al. (2016; see the Electronic Supplementary Material Table S2). For details on the collection of these ecomorphological data, see Alhajeri et al. (2016). ...
Multiple diversification rate shifts explain uneven clade richness in muroid rodents. Previous muroid studies have shown that extrinsic factors, notwithstanding ecological opportunity, are poor predictors of clade diversity. Here, we use a 297-muroid species chronogram that is sampled proportional to total clade diversity, along with various trait-dependent diversification approaches to investigate the association between diversification rates with intrinsic attributes—diet, habitat, body mass, and relative tail length. We found some association between both dietary specialization and body mass, as well as between habitat specialization with relative tail lengths using phylogenetic analyses of variance. However, there was no significant association between diversification rates with the evolution of these traits in muroid rodents. We also show that several of the state-dependent diversification approaches are highly susceptible to Type I error—a result that is in accordance with recent criticisms of these methods. Finally, we discuss several potential causes for the lack of association between the examined trait data with diversification rates, ranging from methodological biases (e.g. method conservativism) to biology (e.g. behavioral plasticity and ecological opportunism of muroid rodents).
... If this is correct, under the theory of adaptive radiation (Schluter 2000), much of phenotypic variation must be linked to a relevant ecological gradient. However, a recent study suggested that muroid morphological diversification seems to be not associated with ecological opportunity, as patterns of DTT show a high within-clade disparity, as opposed to an earlyburst pattern (Alhajeri et al. 2016). Despite the lack of support for ecological opportunity across all muroid clades, support was strongest for sigmodontines (in particular for the predominantly South American subclade Oryzomyalia), and ecological variables were not expressly evaluated (Alhajeri et al. 2016). ...
... However, a recent study suggested that muroid morphological diversification seems to be not associated with ecological opportunity, as patterns of DTT show a high within-clade disparity, as opposed to an earlyburst pattern (Alhajeri et al. 2016). Despite the lack of support for ecological opportunity across all muroid clades, support was strongest for sigmodontines (in particular for the predominantly South American subclade Oryzomyalia), and ecological variables were not expressly evaluated (Alhajeri et al. 2016). ...
... Although sigmodontine morphological variation is not small (Fig. 4; ) when compared with all rodent variation (Samuels 2009) tire tree and within the Oryzomyalia radiation. Debate on how adaptive was the sigmodontine radiation is ongoing (Schenk et al. 2013;Parada et al. 2015;Alhajeri et al. 2016;Tulli et al. 2016), without a clear consensus. We suggest the pattern of high species richness coupled with a lack of clear association between morphological and ecological divergence may be common in rapid rodent radiations (e.g., in the Rattus radiation- Rowe et al. 2011, and in the worldwide muroid radiation- Alhajeri et al. 2016), despite some remarkable instances of rodent convergence involving dietary shifts when distinct radiations are compared (Samuels 2009). ...
Evolutionary radiations on continents are less well understood and appreciated than those occurring on islands. The extent of ecological influence on species divergence can be evaluated to determine whether a radiation was ultimately the outcome of divergent natural selection or else arose mainly by non-ecological divergence. Here, we used phylogenetic comparative methods to test distinct hypotheses corresponding to adaptive and non-adaptive evolutionary scenarios for the morphological evolution of sigmodontine rodents. Results showed that ecological variables (diet and life-mode) explain little of the shape and size variation of sigmodontine skulls and mandibles. A Brownian model with varying rates for insectivory versus all other diets was the most likely evolutionary model. The insectivorous sigmodontines have a faster rate of morphological evolution than mice feeding on other diets, possibly due to stronger selection for features that aid insectivory. We also demonstrate that rapid early-lineage diversification is not accompanied by high morphological divergence among sub-clades, contrasting with island results. The geographic size of continents permits spatial segregation to a greater extent than on islands, allowing for allopatric distributions and escape from interspecific competition. We suggest that continental radiations of rodents are likely to produce a pattern of high species diversification coupled with a low degree of phenotypic specialization. This article is protected by copyright. All rights reserved
... rodent (Burgin et al. 2018(Burgin et al. , 2020Mammal Diversity Database 2022). Such high diversification rates do not seem to be accompanied by a comparable level of adaptive disparity when seen from a macroevolutionary perspective (Carrizo et al. 2014;Alhajeri et al. 2016;Maestri et al. 2017). The adaptive disparity in appendicular morphology (Carrizo et al. 2014;Alhajeri et al. 2016;Coutinho et al. 2017) and the skull and mandible (Maestri et al. 2016(Maestri et al. , 2017 seem to be relatively low and only weakly associated with ecological variables. ...
... Such high diversification rates do not seem to be accompanied by a comparable level of adaptive disparity when seen from a macroevolutionary perspective (Carrizo et al. 2014;Alhajeri et al. 2016;Maestri et al. 2017). The adaptive disparity in appendicular morphology (Carrizo et al. 2014;Alhajeri et al. 2016;Coutinho et al. 2017) and the skull and mandible (Maestri et al. 2016(Maestri et al. , 2017 seem to be relatively low and only weakly associated with ecological variables. Yet, we do not know how empirical disparity is distributed across space and therefore lack information about particular geographic regions where phenotypic disparity may reflect divergent natural selection. ...
Investigations of phenotypic disparity across geography often ignore macroevolutionary processes. As a corollary, the random null expectations to which disparity is compared and interpreted may be unrealistic. We tackle this issue by representing, in geographical space, distinct processes of phenotypic evolution underlying ecological disparity. Under divergent natural selection, assemblages in a given region should have empirical disparity higher than expected under an evolutionarily‐oriented null model, while the opposite may indicate constraints on phenotypic evolution. We gathered phylogenies, biogeographic distributions, and data on the skull morphology of sigmodontine rodents to discover which regions of the Neotropics were more influenced by divergent, neutral, or constrained phenotypic evolution. We found that regions with higher disparity than expected by the evolutionary‐oriented null model, in terms of both size and shape, were concentrated in the Atlantic Forest, suggesting a larger role for divergent natural selection there. Phenotypic disparity in the rest of South America, mainly the Amazon basin, northeastern Brazil and Southern Andes, was constrained — lower than predicted by the evolutionary model. We also demonstrated equivalence between the disparity produced by randomization‐based null models and constrained‐evolution null models. Therefore, including evolutionary simulations into the null modeling framework used in ecophylogenetics can strengthen inferences on the processes underlying phenotypic evolution. This article is protected by copyright. All rights reserved
... Steppan et al. [9] identified four potential areas in the phylogeny where speciation rates accelerated, Fabre et al. [10] identified 24 shifts, and Schenk et al. [1] identified up to 20 shifts. Schenk et al. [1], and later Alhajeri et al. [11], identified the clade Oryzomyalia as resulting from ecological opportunity; however, it was less clear how and why the other clades with accelerated net speciation rates diversified at a higher rate than other muroids. It is also less clear how incomplete taxonomic sampling could influence diversification inference, and it is likely that our estimates will be more accurate as we approach complete sampling of extant species diversity. ...
... An overarching pattern of increasing diversification rate spans across multiple clades and calls for more detailed tests, particularly to quantify to what extent a high background extinction rate may play in producing that pattern. However, diversification analyses here and elsewhere [1,11] still have not provided a clear explanation for the evolutionary success of this clade compared to other mammals. ...
We combined new sequence data for more than 300 muroid rodent species with our previously published sequences for up to five nuclear and one mitochondrial genes to generate the most widely and densely sampled hypothesis of evolutionary relationships across Muroidea. An exhaustive screening procedure for publically available sequences was implemented to avoid the propagation of taxonomic errors that are common to supermatrix studies. The combined data set of carefully screened sequences derived from all available sequences on GenBank with our new data resulted in a robust maximum likelihood phylogeny for 900 of the approximately 1,620 muroids. Several regions that were equivocally resolved in previous studies are now more decisively resolved, and we estimated a chronogram using 28 fossil calibrations for the most integrated age and topological estimates to date. The results were used to update muroid classification and highlight questions needing additional data. We also compared the results of multigene supermatrix studies like this one with the principal published supertrees and concluded that the latter are unreliable for any comparative study in muroids. In addition, we explored diversification patterns as an explanation for why muroid rodents represent one of the most species-rich groups of mammals by detecting evidence for increasing net diversification rates through time across the muroid tree. We suggest the observation of increasing rates may be due to a combination of parallel increases in rate across clades and high average extinction rates. Five increased diversification-rate-shifts were inferred, suggesting that multiple, but perhaps not independent, events have led to the remarkable species diversity in the superfamily. Our results provide a phylogenetic framework for comparative studies that is not highly dependent upon the signal from any one gene.
... The glittery recent ecological and geographical spread of Sigmodontinae in South America and its high extant species accumulation pattern in the Andean region results from an exceptional ecological opportunity on a continental scale, being the most rapid geographically discrete diversification event in mammals 58 . Therefore, this group is an ideal vertebrate model to study the relationship between the Andean surface uplift, diversification, and the notable species accumulation in the Andean regions 55,57,58,61,64,69 . In this study, we aim to evaluate the effect of the Andean mountains on the diversification dynamics and biogeographical history of the Sigmodontinae. ...
The Andean mountains stand out for their striking species richness and endemicity that characterize many emblematic Neotropical clades distributed in or around these mountains. The radiation of the Sigmodontinae subfamily, the most diversified mammalian group in the Neotropics, has been historically related to Andean orogenesis. We aim to evaluate this interplay between geological processes and biological responses through the diversification dynamics, the biogeographical history, and the range evolution of the subfamily. For these, we built the most comprehensive phylogeny and gathered 14,836 occurrences for the subfamily. We identified one shift in the speciation rate in the genus Akodon, which suffered their Andean radiation after the arrival of non-Andean ancestors. Our biogeographic analyses show multiple dispersal paths throughout the evolution that allowed this subfamily to colonize all Neotropics. The Northern Andes and Central-Southern Andes were the most important sources of diversity. In addition, the Central-Southern Andes were the most relevant sink, receiving the highest number of lineages. The Andean region exhibited higher speciation and turnover rates than non-Andean regions. Thus, our results support the crucial role of the Andean Mountains in the Sigmodontinae radiation, acting as a "macroevolutionary cradle" and "species attractor" for several sigmodontine lineages at different times, and as a "species pump" becoming the biogeographic source of multiple widely distributed neotropical lineages. Then, complex macroevolutionary dynamics would explain these rodents' high extant Andean diversity and their wide distribution in the Neotropics.
... Given the unique ecological niche occupied by the Ichthyomyini and the morphological diversity present within the group, in particular when compared to the Sigmodontini, these results are surprising. However, morphological diversity can theoretically be unrelated to rates of diversification (Adams et al., 2009), and comparative analyses across muroid rodents on continents suggests that phylogenetic diversity and phenotypic disparity may be decoupled (Alhajeri, Schenk & Steppan, 2016). For the entire sigmodontine radiation studies have shown the signal of early strong diversification (Fabre et al., 2012, Steppan & Schenk, 2017, much of which may have been associated with biogeographic regional transitions in South America (Schenk & Steppan, 2018). ...
Ichthyomyini, a morphologically distinctive group of Neotropical cricetid rodents, lacks an integrative study of its systematics and biogeography. Since this tribe is a crucial element of the Sigmodontinae, the most speciose subfamily of the Cricetidae, we conducted a study that includes most of its recognized diversity (five genera and 19 species distributed from southern Mexico to northern Bolivia). For this report we analyzed a combined matrix composed of four molecular markers ( RBP3 , GHR , RAG1 , Cytb ) and 56 morphological traits, the latter including 15 external, 14 cranial, 19 dental, five soft-anatomical and three postcranial features. A variety of results were obtained, some of which are inconsistent with the currently accepted classification and understanding of the tribe. Ichthyomyini is retrieved as monophyletic, and it is divided into two main clades that are here recognized as subtribes: one to contain the genus Anotomys and the other composed by the remaining genera. Neusticomys (as currently recognized) was found to consist of two well supported clades, one of which corresponds to the original concept of Daptomys . Accordingly, we propose the resurrection of the latter as a valid genus to include several species from low to middle elevations and restrict Neusticomys to several highland forms. Numerous other revisions are necessary to reconcile the alpha taxonomy of ichthyomyines with our phylogenetic results, including placement of the Cajas Plateau water rat (formerly Chibchanomys orcesi ) in the genus Neusticomys ( sensu stricto ), and the recognition of at least two new species (one in Neusticomys , one in Daptomys ). Additional work is necessary to confirm other unanticipated results, such as the non-monophyletic nature of Rheomys and the presence of a possible new genus and species from Peru. Our results also suggest that ichthyomyines are one of the main Andean radiations of sigmodontine cricetids, with an evolutionary history dating to the Late Miocene and subsequent cladogenesis during the Pleistocene.
... Given the recent radiation of the Tarsomys clade (the crown age of which is less than 2.5 million years old; Fig. 4), the patterns we see within this clade seem to mimic, on a small scale, the diversity of other island-endemic groups in the Indo-Australian archipelago, including Chrotomyini of the Philippines, Hydromyini of Sahul, and Maxomys/Crunomys of Wallacea (sensu Ali and Heaney 2021), in that the species in these clades vary substantially in their ecology based on available natural history information (Heaney et al. , 2016bRowe et al. 2016). Although available relevant ecological information for B. kampalili precludes anything but inferences, the addition of the Tarsomys clade to the growing list of archipelago-endemic murine lineages with morphologically distinct species or genera suggests that ecomorphological diversification may have happened rapidly and consistently across several different Indo-Australian rodent radiations without major shifts in evolutionary tempo or mode among these major clades (Alhajeri et al. 2016;Rowsey et al. 2019;Marcy et al. 2020). Further research on this topic examining morphological evolution among major lineages in the Indo-Australian archipelago clearly is warranted. ...
The Philippine archipelago hosts an exceptional diversity of murid rodents that have diversified following several independent colonization events. Here, we report the discovery of a new species of rodent from Mt. Kampalili on eastern Mindanao Island. Molecular and craniodental analyses reveal this species as a member of a Philippine “New Endemic” clade consisting of Tarsomys, Limnomys, and Rattus everetti (tribe Rattini). This new species of “shrew-mouse” is easily distinguished from its relatives in both craniodental and external characteristics including a long, narrow snout; small eyes and ears; short, dark, dense fur dorsally and ventrally; stout body with a tapering, visibly haired tail shorter than head and body length; stout forepaws; bulbous and nearly smooth braincase; narrow, tapering rostrum; short incisive foramina; slender mandible; and narrow, slightly opisthodont incisors. This new genus and species of murid rodent illustrates that murids of the tribe Rattini have exhibited greater species and morphological diversification within the Philippines than previously known and provides evidence that Mt. Kampalili represents a previously unrecognized center of mammalian endemism on Mindanao Island that is deserving of conservation action.
... Broadly, these methods fall into two classes: supervised approaches, which require an a priori hypothesis of phylogenetic rate variation, and unsupervised approaches, which automatically learn the distribution of phylogenetic rate variation from data. Methodological advances in both types of approaches have made describing patterns of among-lineage evolutionary rate heterogeneity relatively routine, and this in turn has enabled researchers to investigate mechanisms underlying broad-scale differences in phenotypic disparity such as ecological opportunity (Alhajeri et al. 2016; Price et al. 2016), phenotypic integration and modularity (Goswami et al. 2014;Watanabe et al. 2019), and the origin of key innovations (Werner et al. 2014; Barua and Mikheyev 2020;Simões et al. 2020). ...
Understanding phenotypic disparity across the tree of life requires identifying where and when evolutionary rates change on phylogeny. A primary methodological challenge in macroevolution is therefore to develop methods for accurate inference of among-lineage variation in rates of phenotypic evolution. Here, we describe a method for inferring among-lineage evolutionary rate heterogeneity in both continuous and discrete traits. The method assumes that the present-day distribution of a trait is shaped by a variable-rate process arising from a mixture of constant-rate processes and uses a single-pass tree traversal algorithm to estimate branch-specific evolutionary rates. By employing dynamic programming optimization techniques and approximate maximum likelihood estimators where appropriate, our method permits rapid exploration of the tempo and mode of phenotypic evolution. Simulations indicate that the method reconstructs rates of trait evolution with high accuracy. Application of the method to datasets on squamate reptile reproduction and turtle body size recovers patterns of rate heterogeneity identified by previous studies but with computational costs reduced by many orders of magnitude. Our results expand the set of tools available for detecting macroevolutionary rate heterogeneity and point to the utility of fast, approximate methods for studying large scale biodiversity dynamics.
... due to continental colonization or post-extinction free niche space) rather than necessarily ecomorphological diversification (e.g. Alhajeri et al., 2016;Cantalapiedra et al., 2017). Furthermore, the continued ecological importance of therapsids during the Early Triassic may have limited scope for ecological, as opposed to phylogenetic, diversification. ...
Adaptive radiations have played a major role in generating modern and deep-time biodiversity. The Triassic radiation of the Archosauromorpha was one of the most spectacular vertebrate radiations, giving rise to many highly ecomorphologically varied lineages—including the dinosaurs, pterosaurs, and stem-crocodylians—that dominated the larger-bodied land fauna for the following 150 Ma, and ultimately gave rise to today’s > 10,000 species of birds and crocodylians. This radiation provides an outstanding testbed for hypotheses relating to adaptive radiations more broadly. Recent studies have started to characterize the tempo and mode of the archosauromorph early adaptive radiation, indicating very high initial rates of evolution, non-competitive niche-filling processes, and previously unrecognized morphological disparity even among non-crown taxa. However, these analyses rested primarily either on discrete characters or on geometric morphometrics of the cranium only, or even failed to fully include phylogenetic information. Here we expand previous 2D geometric morphometric cranial datasets to include new taxa and reconstructions, and create an analogous dataset of the pelvis, thereby allowing comparison of anatomical regions and the transition from “sprawling” to “upright” posture to be examined. We estimated morphological disparity and evolutionary rates through time. All sampled clades showed a delayed disparity peak for sum of variances and average nearest neighbor distances in both the cranium and pelvis, with disparity likely not saturated by the end of the studied time span (Late Jurassic); this contrasts with smaller radiations, but lends weight to similar results for large, ecomorphologically-varied groups. We find lower variations in pelvic than cranial disparity among Triassic-Jurassic archosaurs, which may be related to greater morphofunctional constraints on the pelvis. Contrasting with some previous work, but also confirming some previous findings during adaptive radiations, we find relatively widespread evidence of correlation between sampled diversity and disparity, especially at the largest phylogenetic scales and using average displacement rather than sum of variances as disparity metric; this also demonstrates the importance of comparing disparity metrics, and the importance of phylogenetic scale. Stem and crown archosauromorphs show a morphological diversification of both the cranium and pelvis with higher initial rates (Permian–Middle Triassic and at the base of major clades) followed by lower rates once diversification into niches has occurred (Late Triassic–Jurassic), indicating an “early burst” pattern sensu lato. Our results provide a more detailed and comprehensive picture of the early archosauromorph radiation and have significant bearing on the understanding of deep-time adaptive radiations more broadly, indicating widespread patterns of delayed disparity peaks, initial correlation of diversity and disparity, and evolutionary early bursts.
... Posiblemente diferentes mecanismos evolutivos independientes han sido los responsables de la diversidad actual (Schenk et al. 2013), por lo que complementario a los forzantes geográficos, los rasgos morfológicos y funcionales de los sigmodontinos que pudieron ser relevantes para la diversificación del grupo, como la adquisición o pérdida de un quinto pliegue molar (Parada et al. 2015), la forma y tamaño craneal en relación al hábito y la dieta (Maestri et al. 2016). No obstante, los resultados no encuentran relación concluyente entre estos y la diversificación, permitiendo que el debate sobre el componente adaptativo de la radiación sigmodontina siga en curso (Schenk et al. 2013;Parada et al. 2015;Alhajeri et al. 2016;Tulli et al. 2016). ...
Taxonomic disparity between close clades is one of the most amazing feature of
biodiversity. A clear example is the rodent subfamily Sigmodontinae (near of 400 species)
and its sister subfamily Tylomyinae (10 species). Tylomyinae is composed by exclusively
arboreal rodents, while Sigmodontinae comprises species with different locomotion types.
For the latter, the most diverse clades are also the richest in cursorial species, that is runner
species associated to open vegetation habitats, environments that covered the major part
of South America during the Upper Miocene. This geological epoch signs the begin of
sigmodontine radiation. Thus, in this research I propose that the cursoriality in
Sigmodontinae acted as a innovación clave triggering the fast generation of new lineages.
This hypothesis predicts that the ancestral lineage inhabited open areas; the temporal
origin of cursoriality is between the Tylomyinae-Sigmodontinae divergence and the
sigmodontine MRCA; and that there is a significant association between cursoriality and
diversification. To assess these predictions, a time-calibrated phylogeny was reconstructed
to infer the diversification pattern for this subfamily allowing to estimate the ancestral
states of the ecomorphological traits and the habitat type, and to evaluate the association
between the cursoriality and diversification. The results obtained reject the hypothesis
proposed due to the non-temporal correspondence of the events, since the cursoriality has
a previous origin to the Tylomyinae-Sigmdontinae diversification (11.6 M.y.). Additionally,
there is not relationship between cursoriality and the Sigmodontinae diversification. Even
so, I propose that cursoriality could have an indirect effect, from the Middle Miocene,
allowing the macroevolutionary success of the sigmodontinae rodents once the open
environments in South America emerged. In this scenario there would be a direct relation
of the diversification with the geographical context rather than with the intrinsic trait
evaluated.
... How many "signatures" (i.e., diet, substrate, thermal tolerance), if any, are superimposed in this bauplan? Fortunately, several recent studies tackled these or related questions using a large quantity of molecular and morphological evidence (e.g., Parada et al. 2015;Alhajeri et al. 2016;Maestri et al. 2016Maestri et al. , 2017Steppan and Schenk 2017). According to Maestri et al. (2017:626) "… ecological variables (diet and life-mode) explain little of the shape and size variation of sigmodontine skulls [sic] and mandibles" and also … insectivorous mice evolve at a faster rate than other groups. ...
While hypsodonty mostly is associated with medium to large body sizes in sigmodontine rodents, highcrowned molars combined with small bodies rarely are recorded. This latter condition is present in Neomicroxus (Sigmodontinae, incertae sedis), a genus of high-Andean cricetids also characterized by a noticeable set of cranial traits, including enlarged turbinals and rostrum, slanting zygomatic plate, and a marked backward displacement of the vertical ramus of the dentary, linked with an enlargement of the basicranial region. These morphological features, combined with the isolated position of this lineage in molecular-based phylogenies, indicate that Neomicroxus should be situated in a new tribe. We name and describe this Páramo novelty monotypic clade here. As a working hypothesis, the hypsodonty displayed by this group is considered an evolutionary response to continued volcanic ash falls that characterized the region during the Neogene. A reappraisal of tribe recognition within the two cricetid largest subfamilies, arvicolines and sigmodontines, is made, coupled with a discussion about the role of morphological convergence in “long-nose” cricetids.
... In our study the very short internode distance hints at rapid radiation early in the Pila lineage (Tsigenopoulos et al., 2003;Han et al., 2004), which might have facilitated random sorting of ancestral alleles, leading to the present case. Rapid radiation can take place in response to increased ecological opportunity such as colonization of a new habitat with available niches (Seehausen, 2006;Sundue et al., 2015, Lajmi & Karanth, 2019; but see Alhajeri et al., 2016). ...
The biota of the Indian subcontinent was assembled through multiple associations with various landmasses during a period spanning the Late Cretaceous to the present. It consists of Gondwanan elements that subsequently dispersed 'out-of-India' and biota that dispersed 'into-India' after the subcontinent collided with Asia. However, the relative contribution of these connections to the current biotic assembly of the subcontinent has been under-explored. Our aim here was to understand the relative importance of these various routes of biotic assembly in India by studying the historical biogeography of the tropical Old World freshwater snail genus Pila. We reconstructed a near-complete phylogeny, based on nuclear and mitochondrial markers, of Ampullariidae including all the described Pila species from India and Ampullariids worldwide. Thereafter, molecular dating and ancestral range estimation analyses were carried out to ascertain the time frame and route of colonization of India by Pila. The results showed that Pila dispersed into India as well as other parts of tropical Asia from Africa after both India and Africa collided with Eurasia. Furthermore, multiple dispersals took place between Southeast Asia and India. These findings corroborate increasing evidence that much of the current Indian assemblage of biota actually dispersed 'into-India' after it collided with Asia. © 2020 The Linnean Society of London, Biological Journal of the Linnean Society.
... First, their radiations would have experienced new extrinsic selection pressures by emigrating from wet tropics to a much drier continent (Aplin and Ford 2014;Smissen and Rowe 2018). Indeed, unlike nearly all other murid radiations, the Australia-New Guinea radiations show some evidence of following an ecological opportunity model (sensu Yoder et al. 2010), where adaptation to new environments, especially dry habitats, could be driving speciation (Schenk et al. 2013;Smissen and Rowe 2018; but see Alhajeri et al. 2016). Furthermore, Australia uniquely lacks other terres-trial placental mammals (Aplin and Ford 2014); therefore, it is possible that a release from competition could allow extrinsic pressures to push murid rodent allometry into morphological niches unavailable to all other murids. ...
Among vertebrates, placental mammals are particularly variable in the covariance between cranial shape and body size (allometry), with rodents being a major exception. Australian murid rodents allow an assessment of the cause of this anomaly because they radiated on an ecologically diverse continent notably lacking other terrestrial placentals. Here, we use 3D geometric morphometrics to quantify species-level and evolutionary allometries in 38 species (317 crania) from all Australian murid genera. We ask whether ecological opportunity resulted in greater allometric diversity compared with other rodents or whether conserved allometry suggests intrinsic constraints and/or stabilizing selection. We also assess whether cranial shape variation follows the proposed rule of craniofacial evolutionary allometry (CREA), whereby larger species have relatively longer snouts and smaller braincases. To ensure we could differentiate parallel versus nonparallel species-level allometric slopes, we compared the slopes of rarefied samples across all clades. We found exceedingly conserved allometry and CREA-like patterns across the 10-million-year split between Mus and Australian murids. This could support both intrinsic-constraint and stabilizing-selection hypotheses for conserved allometry. Large-bodied frugivores evolved faster than other species along the allometric trajectory, which could suggest stabilizing selection on the shape of the masticatory apparatus as body size changes.
... First, their radiations would have experienced new extrinsic selection pressures by immigrating from wet tropics onto a much drier continent (Aplin and Ford 2014;Smissen and Rowe 2018). Indeed, unlike nearly all other murid radiations, the Australia-New Guinea radiations show some evidence of following an ecological opportunity model (sensu Yoder et al. 2010), where adaptation to new environments, especially the dry habitats, could be driving speciation (Schenk et al. 2013;Smissen and Rowe 2018; but see Alhajeri et al. 2016). Furthermore, Australia uniquely lacks other terrestrial placental mammals (Aplin and Ford 2014), therefore it is possible that a release from competition could allow extrinsic pressures to push murid rodent allometry into morphological niches unavailable to all other murids. ...
Among vertebrates, placental mammals are particularly variable in the covariance between their cranial shapes and body size (allometry), with the notable exception of rodents. Australian murid rodents present an opportunity to assess the cause of this anomaly because they radiated on an ecologically diverse continent unique for lacking other terrestrial placentals. Here we used 3D geometric morphometrics to quantify species-level and evolutionary allometries in 38 species (317 crania) from all Australian murid genera. We ask if ecological opportunity resulted in greater allometric diversity; conversely, we test if intrinsic constraints and/or stabilizing selection conserved allometry. To increase confidence in species-level allometric slopes, we introduce a new phylogeny-based method of bootstrapping and randomly resampling across the whole sample. We found exceedingly conserved allometry across the 10 million year split between Mus and the clade containing Australian murids. Cranial shapes followed craniofacial evolutionary allometry (CREA) patterns, with larger species having relatively longer snouts and smaller braincases. CREA is consistent with both intrinsic constraints and stabilizing selection hypotheses for conserved allometry. However, large-bodied frugivores evolved faster, while carnivorous specialists showed skull modifications known to conflict with masticatory efficiency. These results suggest a strong role of stabilizing selection on the masticatory apparatus of murid rodents.
... Regardless of resulting from ancestral or displacementrelated distinction, contemporary chrotomyine morphological variation was likely influenced by phloeomyine incumbency. The emerging picture regarding incumbency effects in the evolution of Indo-Australian rodents is one of strong influence on the resulting ecomorphological diversity of the constituent clades, but weak influence on their rates of lineage diversification [5,20,49] and rates of trait evolution [36,50]. In other words, secondarily colonizing rodent clades appear to be royalsocietypublishing.org/journal/rspb ...
A lineage colonizing a geographic region with no competitors may exhibitrapid diversification due to greater ecological opportunity. The resultantspecies diversity of this primary-colonizing (incumbent) clade may limitsubsequent lineages’ability to persist unless these non-incumbent lineagesare ecologically distinct. We compare the diversity in diet-related mandibu-lar morphology of two sympatric murid rodent clades endemic to LuzonIsland, Philippines—incumbent Phloeomyini and secondary-colonizingChrotomyini—to the mandibular morphological diversity of Sahul Hydro-myini, the sister clade of Chrotomyini and the incumbent murid lineageon the supercontinent of Sahul. This three-clade comparison allows us totest the hypothesis that incumbent lineages can force persistent ecologicaldistinction of subsequent colonists at the time of colonization and through-out the subsequent history of the two sympatric clades. We find thatChrotomyini forms a subset of the diversity of their clade plus Sahul Hydro-myini that minimizes overlap with Phloeomyini. We also infer that thisdifferentiation extends to the stem ancestor of Chrotomyini and SahulHydromyini, consistent with a biotic filter imposed by Phloeomyini. Ourwork illustrates that incumbency has the potential to have a profound influ-ence on the ecomorphological diversity of colonizing lineages at the islandscale even when the traits in question are evolving at similar rates amongindependently colonizing clades.
... Continental systems, being far more complex, are likely to have divergent patterns from those of insular systems given the large area, relatively older age and pre-established biota (Derryberry et al., 2011;Liedtke et al., 2016;Losos & Ricklefs, 2009;Maestri et al., 2016). While some studies point towards the role of ecological opportunity in generating continental adaptive radiations (Barker, Burns, Klicka, Lanyon, & Lovette, 2013;Burbrink et al., 2012;Burbrink & Pyron, 2009;Drummond, Eastwood, Miotto, & Hughes, 2012;McGuire et al., 2014;Price et al., 2014;Schenk, Rowe, & Steppan, 2013), others do not detect the presence of ecological opportunity (Alhajeri & Schenk, 2016;Claramunt, Derryberry, Brumfield, & Remsen, 2012;Day et al., 2013;Derryberry et al., 2011;Liedtke et al., 2016;Schweizer, Hertwig, & Seehausen, 2014;Tran, 2014). Moreover, the relationship between ecological opportunity and the resulting phenotypic diversifications is varied (Derryberry et al., 2011;Garcia-Porta, Šmíd, Sol, Fasola, & Carranza, 2016;Maestri et al., 2016;Pinto, Mahler, & Harmon, 2008), with studies reporting constrained phenotypic diversity in continental systems (Derryberry et al., 2011). ...
The ‘early‐burst’ model of adaptive radiation predicts an early increase in phenotypic disparity concurrent with lineage diversification. Although most studies report a lack of this coupled pattern, the underlying processes are not identified. The continental radiation of Hemidactylus geckos from Peninsular India includes morphologically diverse species that occupy various microhabitats. This radiation began diversifying ~36 Mya with an early increase in lineage diversification. Here, we test the ‘early‐burst’ hypothesis by investigating the presence of ecomorphs and examining the pattern of morphological diversification in a phylogenetic framework. Two ecomorphs— terrestrial and scansorial species— that vary significantly in body size and toepad size were identified. Unlike the prediction of the ‘early‐burst’ model, we find that disparity in toepad morphology accumulated more recently ~14 Mya and fit the OU model. Ancestral state reconstruction of the two ecomorphs demonstrates that terrestrial lineages evolved independently at least five times from scansorial ancestors, with the earliest diversification in terrestrial lineages 19–12 Mya. Our study demonstrates a delayed increase in morphological disparity as a result of the evolution of terrestrial ecomorphs. The diversification of terrestrial lineages is concurrent with the establishment of open habitat and grasslands in Peninsular India, suggesting that the appearance of this novel resource led to the adaptive diversification.
... studies (e.g. Lecompte et al. 2008;Schenk et al. 2013;Alhajeri et al. 2016) have identified Southern Asia as the evolutionary source of this superfamily, which is thought to have colonised the African continent in several immigration events. However, it is evident that African landscapes have played an important role in the Muridae's diversification. ...
Considering the interplay between regional diversification and local community
processes is a relatively nascent field of study. Here, I examined the phylogenetic and
functional structure of African muroid assemblages at both regional (eight bioregions)
and local (72 communities) levels to assess the relative roles of historical processes,
environmental filtering, and ecological interactions in community assembly. In addition,
I used patterns of phylogenetic β diversity and β diversity to separate the factors that
structure muroid assemblages. At the regional scale, none of the regions showed
evidence of phylogenetic evenness, while two of them (Congolian, Southern African)
exhibited phylogenetic structure, probably due to the fact that the opportunity for in situ
speciation has been greater in these biogeographic regions, mostly in the Congolian
rainforests. Functional clustering was detected in the two northernmost regions, where
conditions are more extreme, suggesting the existence of environmental filtering. At a
finer (local) scale, ~6% of the examined muroid communities had Net Relatedness
Index (NRI) values significantly greater than expected by chance (NRI > 2), whereas
no localities harboured muroid communities with NRI values significantly lower than
expected by chance (NRI < -2). Thus, there was no evidence in support of a more
prominent role of competition as the scale decreases. Regional patterns of β diversity
and phylogenetic β diversity suggest that phylogenetic structure in African muroid
assemblages may be explained by the history of speciation and dispersal of this
taxonomic group. Finally, the lack of concordance between phylogenetic and functional
structure highlights the importance of considering the multiple facets of biodiversity to
study community assembly processes from an integrative point of view.
... give rise to impressive radiations of species and high rates of diversification (Rundell and Price 2009, Alhajeri et al. 2016, Maestri et al. 2017. Nonadaptive and adaptive processes offer profoundly different interpretations for patterns of evolutionary radiation (Givnish 2015), but various authors, including (Schenk and Steppan 2018) with sigmodontines, continue to invoke adaptive radiation, despite detailed evidence to the contrary (Maestri et al. 2017). ...
We investigated spatial patterns of evolutionary relatedness and diversification rates to test hypotheses about the historical biogeographic processes underlying the radiation of Neotropical rats and mice (Sigmodontinae, ~400 species). A negative correlation between mean phylogenetic distance and diversification rates of rodent assemblages reveals a pattern of species co‐occurrence in which assemblages of closely related species are also the fastest diversifying ones. Subregions of the Neotropics occupied by distantly related species that are on average more slowly diversifying include Central America, northern South America, and the Atlantic forest. In southern South America, recent species turnover appears to have been higher. Ancestral locations for the main tribes of sigmodontines were also estimated, suggesting eastern South America and the Amazonian lowlands were colonized before some central Andean regions, even though the latter are now centers of species richness for these rodents. Moreover, a past connection between the tropical Andes and the Atlantic Forest is suggested by our results, highlighting a role for a hypothetical arc connecting the two biomes, which would have impacted many other groups of organisms. Whether rapid, recent speciation in some regions is related to Quaternary climatic fluctuations and the young age of sigmodontines (~12.7 Ma crown age) or instead to intrinsic traits of these rodents remains an open question. If the former is true, we hypothesize that contrasting trends will characterize older Neotropical clades.
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... Despite the relative scarcity of studies in which multiple ecologically similar clades have colonized a system, several authors have used this approach to test for incumbency effects at continental scales in birds, fishes, and mammals, examining both rates of lineage diversification (Betancur-R. et al. 2012;Schenk et al. 2013) and morphological evolution (Jønsson et al. 2015;Alhajeri et al. 2016), with mixed support for incumbency affecting diversification. However, the geographic scale at which incumbency may be important in diversification remains an open question. ...
Diversity‐dependent cladogenesis occurs when a colonizing lineage exhibits increasing interspecific competition as it ecologically diversifies. Repeated colonization of a region by closely related taxa may cause similar effects as species within each lineage compete with one another. This may be particularly relevant for secondary colonists, which could experience limited diversification due to competition with earlier, incumbent colonists over evolutionary time. We tested the hypothesis that an incumbent lineage may diminish the diversification of secondary colonists in two speciose clades of Philippine “Old Endemic” murine rodents—Phloeomyini and Chrotomyini—on the relatively old oceanic island of Luzon. Although phylogenetic analyses confirm the independent, non‐contemporaneous colonization of Luzon by the ancestors of these two clades, we found no support for arrested diversification in either. Rather, it appears that diversification of both clades resulted from constant‐rate processes that were either uniform or favored the secondary colonists (Chrotomyini), depending on the method used. Our results suggest that ecological incumbency has not played an important role in determining lineage diversification among Luzon murines, despite sympatric occurrence by constituent species within each lineage, and a substantial head start for the primary colonists.
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... Thereby, lineage and morphological diversification are frequently positively correlated [11,12], but the opposite pattern (i.e., a negative relationship) has also been reported [13,14]. Nevertheless, recent studies have shown that processes underlying phenotypic disparity and those generating species diversity can be uncoupled, suggesting that ecological opportunity is not the only diversification force [15][16][17]. For example, speciation by simple geographic isolation can generate a pattern of declining speciation trough time without the intervention of niche-filling processes [18]. ...
Background: The combination of model-based comparative techniques, disparity analyses and ecomorphological correlations constitutes a powerful method to gain insight into the evolutionary mechanisms that shape morphological variation and speciation processes. In this study, we used a time-calibrated phylogeny of 70 Iberian species of short-horned grasshoppers (Acrididae) to test for patterns of morphological disparity in relation to their ecology and phylogenetic history. Specifically, we examined the role of substrate type and level of ecological specialization in driving different aspects of morphological evolution (locomotory traits, chemosensitive organs and cranial morphology) in this recent radiation.
Results: We found a bimodal distribution of locomotory attributes corresponding to the two main substrate type guilds (plant vs. ground); plant-perching species tend to exhibit larger wings and thicker femora than those that remain on the ground. This suggests that life form (i.e., substrate type) is an important driving force in the evolution of morphological traits in short-horned grasshoppers, irrespective of ancestry. Substrate type and ecological specialization had no significant influence on head shape, a trait that showed a strong phylogenetic conservatism. Finally, we also found a marginal significant association between the length of antennae and the level of ecological specialization, suggesting that the development of sensory organs may be favored in specialist species.
Conclusions: Our results provide evidence that even in taxonomic groups showing limited morphological and ecological disparity, natural selection seems to play a more important role than genetic drift in driving the speciation process. Overall, this study suggests that morphostatic radiations should not necessarily be considered as “non-adaptive” and that the speciation process can bind both adaptive divergence mechanisms and neutral speciation processes related with allopatric and/or reproductive isolation.
... The lack of strength in modelling early bursts by models (except BAMM) was highlighted in the empirical data sets as well, and the EB was often not separated clearly from the BM in terms of relative fit, despite its superior adequacy in modelling temporal rate variation. These results add to the body of ideas advocating that early bursts are often not identified across data sets (Harmon et al., 2010;Slater et al., 2010;Venditti et al., 2011;Alhajeri et al., 2015) not necessarily because such scenarios are scarce in nature, but because current models do not have the power to detect them, and early shifts leave little signal in the tip data . ...
Rates of trait evolution are known to vary across phylogenies, however, standard evolutionary models assume a homogeneous process of trait change. These simple methods are widely applied in small-scale phylogenetic studies whereas models of rate heterogeneity are not, so the prevalence and patterns of potential rate variation in groups up to hundreds of species remains unclear. The extent to which trait evolution is modelled accurately on a given phylogeny is also largely unknown because studies typically lack absolute model fit tests. We investigated these issues by applying both rate-static and variable-rates methods on (i) body mass data for 88 avian clades of 10-318 species, and (ii) data simulated under a range of rate-heterogeneity scenarios. Our results show that rate-heterogeneity is present across small-scaled avian clades, and consequently applying only standard single-process models prompt inaccurate inferences about the generating evolutionary process. Specifically, these approaches underestimate rate-variation, and systematically mislabel temporal trends in trait evolution. Conversely, variable-rates approaches have superior relative fit (they are the best model) and absolute fit (they describe the data well). We show that rate-changes such as single-internal branch variations, rate decreases, and early bursts are hard to detect, even by variable-rates models. We also use recently developed absolute adequacy tests to highlight misleading conclusions based on relative fit alone (e.g. a consistent preference for constrained evolution when isolated terminal branch rate increases are present). This work highlights the potential for robust inferences about trait evolution when fitting flexible models in conjunction with tests for absolute model fit. This article is protected by copyright. All rights reserved.
Dispersal events offer a unique window into macroevolutionary processes, especially with respect to the effects of competition on diversification. Empirical studies testing alternative predictions of competitive effects are often limited in either geographic or phylogenetic scale. Here, we tested some of these hypotheses by comparing an assemblage of 16 oscine passerine clades, representing independent dispersal events into the Western Hemisphere, to their sister clades in the Eastern Hemisphere. We also compared the diversity of this assemblage of clades to an older, incumbent passerine clade in the Western Hemisphere, the suboscines. Specifically, we tested for ecological opportunity and incumbency-mediated constraints by analysis of clade-specific morphological disparities and rates of evolution relative to dispersal history. While there was no consistent outcome of oscine dispersal and macroevolution in the Western Hemisphere relative to their Eastern Hemisphere sister groups, most clades supported a role for ecological opportunity or incumbency effects, and such effects were better explained by differences in species accumulation than by differences in rates of trait evolution or colonization timing. This general pattern was not evident when comparing the entire oscine assemblage of the Western Hemisphere to the incumbent suboscine radiation; oscines and suboscines occupy comparable regions of functional trait diversity and, despite higher rates of trait evolution in oscines, these observations were consistent with simulated null expectations. This result suggests that oscine and suboscine assemblages may have evolved in relative isolation for a significant fraction of their history.
Rodents are the most species-rich order within Mammalia and have evolved disparate morphologies to accommodate numerous locomotor niches, providing an excellent opportunity to understand how locomotor innovation can drive speciation. To evaluate the connection between the evolutionary success of rodents and the diversity of rodent locomotor ecologies, we used a large dataset of proximal limb CT scans from across Myomorpha and Geomyoidea to examine internal and external limb shape. Only fossorial rodents displayed a major reworking of their proximal limbs in either internal or external morphology, with other locomotor modes plotting within a generalist morphospace. Fossorial rodents were also the only locomotor mode to consistently show increased rates of humerus/femur morphological evolution. We propose that these rodent clades were successful at spreading into ecological niches due to high behavioral plasticity and small body sizes, allowing them to modify their locomotor mode without requiring major changes to their proximal limb morphology.
Bipedal hopping is a specialized mode of locomotion that has arisen independently in at least five groups of mammals. We review the evolutionary origins of these groups, examine three of the most prominent hypotheses for why bipedal hopping may have arisen, and discuss how this unique mode of locomotion influences the behavior and ecology of modern species. While all bipedal hoppers share generally similar body plans, differences in underlying musculoskeletal anatomy influence what performance benefits each group may derive from this mode of locomotion. Based on a review of the literature, we conclude that the most likely reason that bipedal hopping evolved is associated with predator avoidance by relatively small species in forested environments. Yet, the morphological specializations associated with this mode of locomotion have facilitated the secondary acquisition of performance characteristics that enable these species to be highly successful in ecologically demanding environments such as deserts. We refute many long-held misunderstandings about the origins of bipedal hopping and identify potential areas of research that would advance the understanding of this mode of locomotion.
The radiation of neotropical echimyid rodents resulted in the diversification of spiny rats, hutias, and the coypu, grouped into four major clades. Different echimyid lineages specialized for terrestrial, semifossorial, semiaquatic, and arboreal locomotion, and for living in bamboo thickets. Comparative phylogenetic methods were herein used for evaluating the relative effect of historical and ecological factors in shaping morphometric traits of external morphology (length of head and body, tail, ear, and hindfeet). Additionally, we investigated whether the adoption of different locomotory habits was associated with changes in their macroevolutionary dynamics. Our findings showed that variation of all traits was phylogenetically structured, although size was less structured than other traits. Tail, ear, and mainly hindfeet were allometrically correlated with head and body length, indicating the occurrence of evolutionary structural constraints. In addition to phylogenetic and allometric components, morphometric variation was strongly associated with locomotory specializations, except for body size. Disparification of body size and tail length took place gradually, fitting the Brownian motion model albeit with some punctual shifts in evolutionary rates. Some of these shifts were associated with changes in locomotory habits, notably with adoption of a semiaquatic habit by the large-sized Myocastor lineage, which occurred with an accelerated rate of size evolution. Evolutionary changes in ear and hindfeet length were concentrated during early echimyid diversification, concomitantly with the emergence of most locomotory habits, with subsequent deceleration of evolutionary rates. These findings indicated a complex interaction between phylogenetic, structural, and ecological effects gradually shaping echimyid external morphology.
The Australasian marsupial family Dasyuridae exhibits one of the most spectacular species-level diversity of any marsupial group. The existence of such exceptional species and phenotypic diversity is commonly attributed to ecological opportunity (EO). According to the EO hypothesis, organisms freed from the burden of competition may undergo an initial burst in diversification and morphological evolution. Subsequently, as accessible niches become occupied, rates of diversification should slow through time. We examined dynamics of lineage and phenotypic diversification in order to test whether Dasyuridae diversified in a classic adaptive radiation. We found that patterns of both lineage diversification and phenotypic (body mass) disparity exhibited an early burst (EB) as predicted by the EO model. Three historical events may have spurred this radiation: the extinction of thylacinids, the emergence of the New Guinean cordillera, and the spread of arid habitats as evidenced by the existence of phylogenetic clustering in these regions. In contrast to previous studies carried out in continent-wide systems, our results support a niche-filling scenario with an EB signal strong enough to be detected. This study shows that the Dasyuridae diversification fully conforms to the postulates of the EO hypothesis and thus, it constitutes a “classic” adaptive radiation.
The niche-filling process predicted by the 'ecological opportunity' (EO) model is an often-invoked mechanism for generating exceptional diversity in island colonizers. Whether the same process governs lineage accumulation and trait disparity during continental colonization events is less clear. Here we test this prediction by investigating the rate dynamics and trait evolution of one of Africa's most widespread amphibian colonizers, the true toads (Bufonidae). By reconstructing the most complete molecular phylogeny of African Bufonidae to date, we find that the diversification of lineages in Africa best conforms to a constant rate model throughout time and across subclades, with little support for EO. Evolutionary rates of life history traits have similarly been constant over time. However, an analysis of generalists and specialists showed a shift towards higher speciation rates associated with habitat specialization. The overall lack of EO signal can be interpreted in a number of ways and we propose several explanations. Firstly, methodological issues might preclude the detection of EO. Secondly colonizers might not experience true EO conditions and due to the size, ecological heterogeneity and age of landmasses, the diversification processes might be more complex. Thirdly lower speciation rates of habitat generalists may have affected overall proliferation of lineages. This article is protected by copyright. All rights reserved.
The Late Miocene to Pleistocene North American genus Bensonomys is recognized as a subgenus of the Pleistocene and Recent South American genus Calomys. Two new species of Calomys are described from the Hemphillian White Cone fauna of Arizona. Characters of this older material indicate that Calomys is derived from Copemys, the cricetine which is also ancestral to Peromyscus. The phyllotine group of South American cricetines initially evolved in North America and did not enter South America until the Panamanian land bridge was established, in the latest Pliocene or earliest Pleistocene.
The Great American Biotic Interchange (GABI) was greatly influenced by the completion of the Isthmus of Panama and impacted the composition of modern faunal assemblages in the Americas. However, the contribution of preceding events has been comparatively less explored, even though early immigrants in the fossil records are evidence for waif dispersals. The cricetid rodents of the subfamily Sigmodontinae are a classic example of a species-rich South American radiation resulting from an early episode of North American invasion. Here, we provide a temporal and spatial framework to address key aspects of the historical biogeography and diversification of this diverse mammal group by using mitochondrial and nuclear DNA datasets coupled with methods of divergence time estimation, ancestral area reconstruction and comparative phylogenetics. Relaxed-clock time estimates indicate that divergence of the Sigmodontinae began in the middle-late Miocene (ca. 12-9 Ma). Dispersal-vicariance analyses point to the arrival of a single lineage of northern invaders with a widespread ancestral distribution and imply that the initial differentiation between Central and South America gave rise to the most basal groups within the subfamily. These two major clades diversified in the late Miocene followed by the radiation of main tribes until the early Pliocene. Within the Oryzomyalia, tribes diverged initially in eastern South America whereas multiple dispersals into the Andes promoted further diversification of the majority of modern genera. A comparatively uniform background tempo of diversification explains the species richness of sigmodontines across most nodes, except for two akodontine genera with recent increases in diversification rates. The bridging of the Central American seaway and episodes of low sea levels likely facilitated the invasion of South America long before the onset of the post-Isthmian phase of the GABI.
Speciation generally involves a three-step process-range expansion, range fragmentation and the development of reproductive isolation between spatially separated populations. Speciation relies on cycling through these three steps and each may limit the rate at which new species form. We estimate phylogenetic relationships among all Himalayan songbirds to ask whether the development of reproductive isolation and ecological competition, both factors that limit range expansions, set an ultimate limit on speciation. Based on a phylogeny for all 358 species distributed along the eastern elevational gradient, here we show that body size and shape differences evolved early in the radiation, with the elevational band occupied by a species evolving later. These results are consistent with competition for niche space limiting species accumulation. Even the elevation dimension seems to be approaching ecological saturation, because the closest relatives both inside the assemblage and elsewhere in the Himalayas are on average separated by more than five million years, which is longer than it generally takes for reproductive isolation to be completed; also, elevational distributions are well explained by resource availability, notably the abundance of arthropods, and not by differences in diversification rates in different elevational zones. Our results imply that speciation rate is ultimately set by niche filling (that is, ecological competition for resources), rather than by the rate of acquisition of reproductive isolation.
Exceptional species and phenotypic diversity commonly are attributed to ecological opportunity (EO). The conventional EO model predicts that rates of lineage diversification and phenotypic evolution are elevated early in a radiation only to decline later in response to niche availability. Foregut fermentation is hypothesized to be a key innovation that allowed colobine monkeys (subfamily Colobinae), the only primates with this trait, to successfully colonize folivore adaptive zones unavailable to other herbivorous species. Therefore, diversification rates also are expected to be strongly linked with the evolution of traits related to folivory in these monkeys. Using dated molecular phylogenies and a dataset of feeding morphology, I test predictions of the EO model to evaluate the role of EO conferred by foregut fermentation in shaping the African and Asian colobine radiations. Findings from diversification methods coupled with colobine biogeographic history provide compelling evidence that decreasing availability of new adaptive zones during colonization of Asia together with constraints presented by dietary specialization underlie temporal changes in diversification in the Asian but not African clade. Additionally, departures from the EO model likely reflect iterative diversification events in Asia.
A number of methods have been developed to infer differential rates of species diversification through time and among clades using time-calibrated phylogenetic trees. However, we lack a general framework that can delineate and quantify heterogeneous mixtures of dynamic processes within single phylogenies. I developed a method that can identify arbitrary numbers of time-varying diversification processes on phylogenies without specifying their locations in advance. The method uses reversible-jump Markov Chain Monte Carlo to move between model subspaces that vary in the number of distinct diversification regimes. The model assumes that changes in evolutionary regimes occur across the branches of phylogenetic trees under a compound Poisson process and explicitly accounts for rate variation through time and among lineages. Using simulated datasets, I demonstrate that the method can be used to quantify complex mixtures of time-dependent, diversity-dependent, and constant-rate diversification processes. I compared the performance of the method to the MEDUSA model of rate variation among lineages. As an empirical example, I analyzed the history of speciation and extinction during the radiation of modern whales. The method described here will greatly facilitate the exploration of macroevolutionary dynamics across large phylogenetic trees, which may have been shaped by heterogeneous mixtures of distinct evolutionary processes.
The tropical Andes and Amazon are among the richest regions of endemism for mammals, and each has given rise to extensive in situ radiations. Various animal lineages have radiated ex situ after colonizing one of these regions from the other: Amazonian clades of dendrobatid frogs and passerine birds may have Andean ancestry, and transitions from the Amazon to Andes may be even more common. To examine biogeographic transitions between these regions, we investigated the evolutionary history of three clades of rodents in the family Echimyidae: bamboo rats (Dactylomys-Olallamys-Kannabateomys), spiny tree-rats (Mesomys-Lonchothrix), and brush-tailed rats (Isothrix). Each clade is distributed in both the Andes and Amazonia, and is more diverse in the lowlands. We used two mitochondrial (cyt-b and 12S) and three nuclear (GHR, vWF, and RAG1) markers to reconstruct their phylogenetic relationships. Tree topologies and ancestral geographic ranges were then used to determine whether Andean forms were basal to or derived from lowland radiations.
Four biogeographic transitions are identified among the generic radiations. The bamboo rat clade unambiguously originated in the Amazon ca. 9 Ma, followed by either one early transition to the Andes (Olallamys) and a later move to the Amazon (Dactylomys), or two later shifts to the Andes (one in each genus). The Andean species of both Dactylomys and Isothrix are sister to their lowland species, raising the possibility that highland forms colonized the Amazon Basin. However, uncertainty in their reconstructed ancestral ranges obscures the origin of these transitions. The lone Andean species of Mesomys is confidently nested within the lowland radiation, thereby indicating an Amazon-to-Andes transition ca. 2 Ma.
Differences in the timing of these biogeographic transitions do not appear to explain the different polarities of these trees. Instead, even within the radiation of a single family, both Andean and Amazonian centers of endemism appear enriched by lineages that originated in the other region. Our survey of other South American lineages suggests a pattern of reciprocal exchange between these regions---among mammals, birds, amphibians, and insects we found no fewer than 87 transitions between the Andes and Amazon from Miocene-Pleistocene. Because no clear trend emerges between the timing and polarity of transitions, or in their relative frequency, we suggest that reciprocal exchange between tropical highland and lowland faunas in South America has been a continual process since ca. 12 Ma.
Playing the Tape of Life
Should the tape of life be replayed, would it produce the same music? Many influential evolutionary biologists, notably Stephen J. Gould, have argued that the answer is “no.” However, patterns of convergence among different species filling similar niches all over the world have argued that the answer is neither so simple nor perhaps so negative. Classic cases of convergence, such as marsupials on the Australian continent or cichlids across the African rift lakes, have demonstrated that similar ecological pressures can result in species with similar ecological traits. Such classic examples, however, do not allow for the influence of niche filling based purely on chance. Mahler et al. (p. 292 ) take advantage of the well-studied species clades of Caribbean anoles to examine patterns of adaptation and niche filling across species and islands. Across-islands convergence on a few distinct adaptive peaks (or niches) has driven diversification of species. Anomalies from these ecotypes are only found on the largest, most diverse islands. Thus, ecological niches powerfully shape species and convergence on particular forms is an inherent component of adaptation. Thus, it seems that the tape of life might play the same music, despite being produced by different instruments.
https://cran.r-project.org/package=coda
Several evolutionary theories predict that rates of morphological change should be positively associated with the rate at which new species arise. For example, the theory of punctuated equilibrium proposes that phenotypic change typically occurs in rapid bursts associated with speciation events. However, recent phylogenetic studies have found little evidence linking these processes in nature. Here we demonstrate that rates of species diversification are highly correlated with the rate of body size evolution across the 30,000+ living species of ray-finned fishes that comprise the majority of vertebrate biological diversity. This coupling is a general feature of fish evolution and transcends vast differences in ecology and body-plan organization. Our results may reflect a widespread speciational mode of character change in living fishes. Alternatively, these findings are consistent with the hypothesis that phenotypic 'evolvability'-the capacity of organisms to evolve-shapes the dynamics of speciation through time at the largest phylogenetic scales.
This is the first cladistic analysis of sigmodontine rodents (Cricetidae, Sigmodontinae) based on nuclear and mitochondrial DNA sequences. Two most parsimonious cladograms (7410 steps in length; CI = 0.199; RI = 0.523) were discovered. Sig-modontinae appears well supported. Sigmodon is sister to the remaining living sigmodontines. It is shown that Euneomys is not a phyllotine and that the Reithrodon group is not monophyletic. Results corroborate that the abrothricines form a natural group that is not part of the akodont radiation. The akodontine tribe is well supported, and is composed of five main clades, whose limits and relationships are thoroughly discussed. For instance, the scapteromyines do not form a natural group and they fall within the akodontine clade. Additionally, I present some taxonomic judgments and comments on the historical biogeography of sigm-odontines in the light of the newly discovered relationships. For example, five akodontine divisions are suggested: the Akodon, the Bibimys, the Blarinomys, the Oxymycterus, and the Scapteromys Divisions. It is shown that traditional hypotheses of sigmodontine historical biogeography are falsified by the recovered topology.
Here, we present a comprehensive phylogenetic analysis based on nuclear and mitochondrial DNA sequences of rodents of the subfamily Sigmodontinae. The emphasis is placed on the large tribe Phyllotini; sampling includes for the first time in any molecular-based phylogenetic analysis representatives of several genera traditionally considered to be phyllotines. Given the broad taxonomic sampling, results provide substantial improvements in our knowledge on both the structure of the sigmodontine radiation and of phyllotine phylogenetic relationships. For instance, the tribe Ichthyomyini was not recovered monophyletic. Similarly, in a novel hypothesis on the contents of the tribe Phyllotini, it is shown that unlike Galenomys, the genera Chinchillula, Neotomys and Punomys are not phyllotines. The later genera together with Andinomys, Euneomys, Irenomys and Juliomys form part of novel generic clades of mostly Andean sigmodontine rodents. More in general, results strongly suggest the occurrence of several instances of putative morphological convergence among distinct sigmodontine lineages (e.g. among now considered to be ichthyomyines; between Phyllotini and some Andean taxa; among Euneomys-Neotomys and Reithrodon). Finally, we suggest that the historical biogeography of the sigmodontine rodents is far more complex than earlier envisioned.
Phylogenetic Principal Components Analysis (pPCA) is a recently proposed method for ordinating multivariate data in a way that takes into account the phylogenetic non-independence among species means. We review this method in terms of geometric morphometric shape analysis and compare its properties to ordinary principal components analysis (PCA). We find that pPCA produces a shape space that preserves the Procrustes distances between objects, that allows shape models to be constructed, and that produces scores that can be used as shape variables for most purposes. Unlike ordinary PCA scores, however, the scores on pPC axes are correlated with one another and their variances do not correspond to the eigenvalues of the phylogenetically corrected axes. The pPC axes are oriented by the non-phylogenetic component of shape variation, but the positioning of the scores in the space retains phylogenetic covariance making the visual information presented in plots a hybrid of non-phylogenetic and phylogenetic. Presuming that all pPCA scores are used as shape variables, there is no difference between them and PCA scores for the construction of distance-based trees (such as UPGMA), for morphological disparity, or for ordinary multivariate statistical analyses (so long as the algorithms are suitable for correlated variables). pPCA scores yield different trait-based trees (such as maximum likelihood trees for continuous traits) because the scores are correlated and because the pPC axes differ from PC axes. pPCA eigenvalues represent the residual shape variance once the phylogenetic covariance has been removed (though there are scaling issues), and as such they provide information on covariance that is independent of phylogeny. Tests for modularity on pPCA eigenvalues will therefore yield different results than ordinary PCA eigenvalues. pPCA can be considered another tool in the kit of geometric morphometrics, but one whose properties are more difficult to interpret than ordinary PCA.
Describes the models and methodology of scaling studies, though various examples (the -3/2 self-thinning law in plants; Cope's Law, that species within a lineage trend towards larger body size with evolutionary time; and scaling of home range and population density in mammals) suggest that they do not give much precision in their predictions for individuals or species. However, they do throw light on a lot of important issues. -S.J.Yates
Background
Development of phylogenetic methods that do not rely on fossils for the study of evolutionary processes through time have revolutionized the field of evolutionary biology and resulted in an unprecedented expansion of our knowledge about the tree of life. These methods have helped to shed light on the macroevolution of many taxonomic groups such as the placentals (Mammalia). However, despite the increase of studies addressing the diversification patterns of organisms, no synthesis has addressed the case of the most diversified mammalian clade: the Rodentia.
Results
Here we present a rodent maximum likelihood phylogeny inferred from a molecular supermatrix. It is based on 11 mitochondrial and nuclear genes that covers 1,265 species, i.e., respectively 56% and 81% of the known specific and generic rodent diversity. The inferred topology recovered all Rodentia clades proposed by recent molecular works. A relaxed molecular clock dating approach provided a time framework for speciation events. We found that the Myomorpha clade shows a greater degree of variation in diversification rates than Sciuroidea, Caviomorpha, Castorimorpha and Anomaluromorpha. We identified a number of shifts in diversification rates within the major clades: two in Castorimorpha, three in Ctenohystrica, 6 within the squirrel-related clade and 24 in the Myomorpha clade. The majority of these shifts occurred within the most recent familial rodent radiations: the Cricetidae and Muridae clades. Using the topological imbalances and the time line we discuss the potential role of different diversification factors that might have shaped the rodents radiation.
Conclusions
The present glimpse on the diversification pattern of rodents can be used for further comparative meta-analyses. Muroid lineages have a greater degree of variation in their diversification rates than any other rodent group. Different topological signatures suggest distinct diversification processes among rodent lineages. In particular, Muroidea and Sciuroidea display widespread distribution and have undergone evolutionary and adaptive radiation on most of the continents. Our results show that rodents experienced shifts in diversification rate regularly through the Tertiary, but at different periods for each clade. A comparison between the rodent fossil record and our results suggest that extinction led to the loss of diversification signal for most of the Paleogene nodes.
Abstract Coral reef fishes represent one of the most spectacularly diverse assemblages of vertebrates on the planet, but our understanding of their mode of diversification remains limited. Here we test whether the diversity of the damselfishes (Pomacentridae), one of the most species-rich families of reef-associated fishes, was produced by a single or multiple adaptive radiation(s) during their evolutionary history. Tests of the tempo of lineage diversification using a time-calibrated phylogeny including 208 species revealed that crown pomacentrid diversification has not slowed through time as expected under a scenario of a single adaptive radiation resulting from an early burst of diversification. Evolutionary modeling of trophic traits similarly rejected the hypothesis of early among-lineage partitioning of ecologically important phenotypic diversity. Instead, damselfishes are shown to have experienced iterative convergent radiations wherein subclades radiate across similar trophic strategies (i.e., pelagic feeders, benthic feeders, intermediate) and morphologies. Regionalization of coral reefs, competition, and functional constraints may have fueled iterative ecological radiation and convergent evolution of damselfishes. Through the Pomacentridae, we illustrate that radiations may be strongly structured by the nature of the constraints on diversification.
Adaptive radiation (AR) theory predicts that groups sharing the same source of ecological opportunity (EO) will experience deterministic species diversification and morphological evolution. Thus, deterministic ecological and morphological evolution should be correlated with deterministic patterns in the tempo and mode of speciation for groups in similar habitats and time periods. We test this hypothesis using well-sampled phylogenies of four squamate groups that colonized the New World (NW) in the Late Oligocene. We use both standard and coalescent models to assess species diversification, as well as likelihood models to examine morphological evolution. All squamate groups show similar early pulses of speciation, as well as diversity-dependent ecological limits on clade size at a continental scale. In contrast, processes of morphological evolution are not easily predictable and do not show similar pulses of early and rapid change. Patterns of morphological and species diversification thus appear uncoupled across these groups. This indicates that the processes that drive diversification and disparification are not mechanistically linked, even among similar groups of taxa experiencing the same sources of EO. It also suggests that processes of phenotypic diversification cannot be predicted solely from the existence of an AR or knowledge of the process of diversification.
https://cran.r-project.org/package=coda
An important dimension of adaptive radiation is the degree to which diversification rates fluctuate or remain constant through time. Focusing on plethodontid salamanders of the genus Desmognathus, we present a novel synthetic analysis of phylogeographic history, rates of ecomorphological evolution and species accumulation, and community assembly in an adaptive radiation. Dusky salamanders are highly variable in life history, body size, and ecology, with many endemic lineages in the southern Appalachian Highlands of eastern North America. Our results show that life-history evolution had important consequences for the buildup of plethodontid-salamander species richness and phenotypic disparity in eastern North America, a global hot spot of salamander biodiversity. The origin of Desmognathus species with aquatic larvae was followed by a high rate of lineage accumulation, which then gradually decreased toward the present time. The peak period of lineage accumulation in the group coincides with evolutionary partitioning of lineages with aquatic larvae into seepage, stream-edge, and stream microhabitats. Phylogenetic simulations demonstrate a strong correlation between morphology and microhabitat ecology independent of phylogenetic effects and suggest that ecomorphological changes are concentrated early in the radiation of Desmognathus. Deep phylogeoggraphic fragmentation within many codistributed ecomorph clades suggests long-term persistence of ecomorphological features and stability of endemic lineages and communities through multiple climatic cycles. Phylogenetic analyses of community structure show that ecomorph o logical divergence promotes the coexistence of lineages and that repeated, independent evolution of ruicrohabitat-associated ecomorphs has a limited role in the evolutionary assembly of Desniognathus communities. Comparing and contrasting our results to other adaptive radiations having different biogeographic histories, our results suggest that rates of diversification during adaptive radiation are intimately linked to the degree to which community structure persists over evolutionary time.
The Muroidea include most of the diverse mouse-like rodents living today. The extant families of muroid rodents recognized by us are Muridae (true rats and mice), Cricetidae (hamsters, diverse hypsodont groups, and many American lineages), Gerbillidae (gerbils, sand rats and jirds) and several smaller groups, most of which have been given familial rank elsewhere. These are Nesomyidae (including Afrocricetodontinae), Rhizomyidae, Dendromuridae, Petromyscidae, Spalacidae, Cricetomyidae, Platacanthomyidae, and Lophiomyidae. Arvicoline (microtine) genera are not considered to constitute a family because they are late derivatives of advanced cricetids and because they form a polyphyletic group (C. A. Repenning, personal communication).
Explaining variation in species richness among provinces and other large geographic regions remains one of the most challenging problems at the intersection of ecology and evolution. Here we argue that empirical evidence supports a model whereby ecological factors associated with resource availability regulate species richness at continental scales. Any large-scale predictive model for biological diversity must explain three robust patterns in the natural world. First, species richness for evolutionary biotas is highly correlated with resource-associated surrogate variables, including area, temperature, and productivity. Second, species richness across epochal timescales is largely stationary in time. Third, the dynamics of diversity exhibit clear and predictable responses to mass extinctions, key innovations, and other perturbations. Collectively, these patterns are readily explained by a model in which species richness is regulated by diversity-dependent feedback mechanisms. We argue that many purported tests of the ecological limits hypothesis, including branching patterns in molecular phylogenies, are inherently weak and distract from these three core patterns. We have much to learn about the complex hierarchy of processes by which local ecological interactions lead to diversity dependence at the continental scale, but the empirical evidence overwhelmingly suggests that they do.
Most existing methods for modeling trait evolution are univariate, while researchers are often interested in investigating evolutionary patterns and processes across multiple traits. Principal components analysis (PCA) is commonly used to reduce the dimensionality of multivariate data as univariate trait models can be fit to the individual principal components. The problem with using standard PCA on phylogenetically structured data has been previously pointed out yet it continues to be widely used in the literature. Here we demonstrate precisely how using standard PCA can mislead inferences: the first few principal components of traits evolved under constant-rate multivariate Brownian motion will appear to have evolved via an "early burst" process. A phylogenetic PCA (pPCA) has been proprosed to alleviate these issues. However, when the true model of trait evolution deviates from the model assumed in the calculation of the pPCA axes, we find that the use of pPCA suffers from similar artifacts as standard PCA. We show that datasets with high effective dimensionality are particularly likely to lead to erroneous inferences. Ultimately, all of the problems we report stem from the same underlying issue-by considering only the first few principal components as univariate traits, we are effectively examining a biased sample of a multivariate pattern. These results highlight the need for truly multivariate phylogenetic comparative methods. As these methods are still being developed, we discuss potential alternative strategies for using and interpreting models fit to univariate axes of multivariate data.
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George Gaylord Simpson famously postulated that much of life’s diversity originated as adaptive radiations—more or less simulta- neous divergences of numerous lines from a single ancestral adaptive type. However, identifying adaptive radiations has proven difficult due to a lack of broad-scale comparative datasets. Here, we use phylogenetic comparative data on body size and shape in a diversity of animal clades to test a key model of adaptive radiation, in which initially rapid morphological evolution is followed by relative stasis. We compared the fit of this model to both single selective peak and random walk models. We found little support for the early-burst model of adaptive radiation, whereas both other models, particularly that of selective peaks, were commonly supported. In addition, we found that the net rate of morphological evolution varied inversely with clade age. The youngest clades appear to evolve most rapidly because long-term change typically does not attain the amount of divergence predicted from rates measured over short time scales. Across our entire analysis, the dominant pattern was one of constraints shaping evolution continually through time rather than rapid evolution followed by stasis. We suggest that the classical model of adaptive radiation, where morphological evolution is initially rapid and slows through time, may be rare in comparative data.
Eisenberg and Wilson (Evolution, 32:740-751, 1978) have documented an interesting relationship between the relative brain size of bats and the complexity of the habitat in which they forage. They found that bats that fly and forage through foliage have larger brains relative to their body size than those that forage in open air. Their explanation was that bats in the complex habitat must process more complex sonic information to navigate through the foliage. In order to do this a larger brain is required. The Peromyscus of North America may offer a similar paradigm as far as habitat complexity is concerned. Species of this genus can be found associated with a variety of habitats: forest, brushlands, rock slides, and grasslands. It seems reasonable that these structurally different habitats may require different climbing abilities by the Peromyscus inhabitants. If functioning in a structurally complex habitat requires a relatively larger brain to process information than is required in a structurally simple habitat, then, following the logic of Eisenberg and Wilson (1978), those species that are good climbers will have relatively larger brains than species that are poor climbers. If this hypothesis is correct, such a pattern of morphological variation in brain size may be expected intraspecifically in P. maniculatus and P. leucopus, two species that occur in a wide varietv of habitats throughout their range.
Understanding the dynamics of speciation, extinction and phenotypic evolution is a central challenge in evolutionary biology. Here, we present BAMM tools, an r package for the analysis and visualization of macroevolutionary dynamics on phylogenetic trees. BAMM tools is a companion package to BAMM , an open‐source program for reversible‐jump MCMC analyses of diversification and trait evolution.
Functions in BAMM tools operate directly on output from the BAMM program. The package is oriented towards reconstructing and visualizing changes in evolutionary rates through time and across clades in a Bayesian statistical framework.
BAMM tools enables users to extract credible sets of diversification shifts and to identify diversification histories with the maximum a posteriori probability. Users can compare the fit of alternative diversification models using Bayes factors and by directly comparing model posterior probabilities.
By providing a robust framework for quantifying uncertainty in macroevolutionary dynamics, BAMM tools will facilitate inference on the complex mixture of processes that have shaped the distribution of species and phenotypes across the tree of life.
The 27 species of Dendroica wood-warblers represent North America's most spectacular avian adaptive radiation. Dendroica species exhibit high levels of local sympatry and differ in plumage and song, but the group contrasts with other well–know avian adaptive radiations such as the Hawaiian honeycreepers and Galapagos finches in that Dendroica species have differentiated modestly in morphometric traits related to foraging. Instead, sympatric Dendroica tend to partition resources behaviourally and they have become a widely cited example of competitive exclusion. We explore the temporal structure of Dendroica diversification via a phylogeny based on 3639 nucleotides of protein–coding mitochondrial DNA (mtDNA). The taxa sampled include 60 individuals representing 24 Dendroica species and a variety of other paruline warbler and outgroup species. Mitochondrial divergences among Dendroica species were generally large (mean pairwise interspecific distances, 10.0%) and many species were rooted in a basal polytomy.
The prevalence of long terminal branches indicates that these species have evolved efficient isolating mechanisms that hav prevented mtDNA introgression despite the many opportunities for hybridization resulting from local sympatry. Comparison with a null model of random bifurcation–extinction demonstrate that cladogenesis in Dendroica has been clustered non–randomly with respect to time, with a significant burst of speciation occurring early in the histor of the genus, possibly as long ago as the Late Miocene or Early Pliocene periods. Although this non–random clustering of speciatio is consistent with the pattern expected of an adaptive radiation, the age of the Dendroica radiation suggests it is an ‘ancient species flock’ in which most extant species represent lineages that have long been evolutionaril independent.
Studies of phylogenetic diversification often show evidence for slowdowns in diversification rates over the history of clades. Recent studies seeking biological explanations for this pattern have emphasized the role of niche differentiation, as in hypotheses of adaptive radiation and ecological limits to diversity. Yet many other biological explanations might underlie diversification slowdowns. In this paper, we focus on the geographic context of diversification, environment-driven bursts of speciation, failure of clades to keep pace with a changing environment, and protracted speciation. We argue that, despite being currently underemphasized, these alternatives represent biologically plausible explanations that should be considered along with niche differentiation. Testing the importance of these alternative hypotheses might yield fundamentally different explanations for what influences species richness within clades through time.
Aim
The Neotropical parrots (Arini) are an unusually diverse group which colonized South America in the Oligocene. The newly invaded Neotropics may have functioned as an underused adaptive zone and provided novel ecological opportunities that facilitated diversification. Alternatively, diversification may have been driven by ecological changes caused by Andean uplift and/or climate change from the Miocene onwards. Our aim was to find out whether Arini diversified in a classical adaptive radiation after their colonization of South America, or whether their diversification occurred later and was influenced by more recent environmental change.
Location
Neotropics.
Methods
We generated a time‐calibrated phylogeny of more than 80% of all Arini species in order to analyse lineage diversification. This chronogram was also used as the basis for the reconstruction of morphological evolution within Arini using a multivariate ratio analysis of three size measurements.
Results
We found a concentration of size evolution and partitioning of size niches in the early history of Arini consistent with the process of adaptive radiation, but there were no signs of an early burst of speciation or a decrease in speciation rates through time. Although we detected no overall temporal shifts in diversification rates, we discovered two young, unexpectedly species‐rich clades.
Main conclusions
Arini show signs of an early adaptive radiation, but we found no evidence of the slowdown in speciation rate generally considered a feature of island or lake radiations. Historical processes and environmental change from the Miocene onwards may have kept diversification rates roughly constant ever since the colonization of the Neotropics. Thus, Arini may not yet have reached equilibrium diversity. The lack of diversity‐dependent speciation might be a general feature of adaptive radiations on a continental scale, and diversification processes on continents might therefore not be as ecologically limited as in isolated lakes or on oceanic islands.
Why some clades are more species-rich than others is a central question in macroevolution. Most hypotheses explaining exceptionally diverse clades involve the emergence of an ecological opportunity caused by a major biogeographic transition or evolution of a key innovation. The radiation of muroid rodents is an ideal model for testing theories of diversification rates in relation to biogeography and ecological opportunity because the group is exceptionally species-rich (comprising nearly one-third of all mammal species), it is ecologically diverse, and it has colonized every major landmass except New Zealand and Antarctica, thus providing multiple replicate radiations. We present an extension of the conventional ecological opportunity model to include a geographic incumbency effect, develop the largest muroid phylogeny to date, and use this phylogeny to test the new model. The nearly 300-species phylogeny based on four nuclear genes is robustly resolved throughout. Consistent with the fossil record, we identified Eurasia as the most likely origin of the group and reconstructed five to seven colonizations of Africa, five of North America, four of Southeast Asia, two of South America, two of Sahul, one of Madagascar, and eight to ten recolonizations of Eurasia. We accounted for incomplete taxon sampling by using multiple statistical methods and identified three corroborated regions of the tree with significant shifts in diversification rates. In several cases, higher rates were associated with the first colonization of a continental area, but most colonizations were not followed by bursts of speciation. We found strong evidence for diversification consistent with the ecological opportunity model (initial burst followed by density-dependent slowdown) in the first colonization of South America and partial support for this model in the first colonization of Sahul. Primary colonizers appear to inhibit the ultimate diversity of secondary colonizers, a pattern of incumbency that is consistent with ecological opportunity, but they did not inhibit initial diversification rates of secondary colonizers. These results indicate that ecological opportunity may be a general but weak process in muroids and one that requires specific circumstances to lead to an adaptive radiation. The total land area, length of time between colonizations, and rank of colonizations did not influence the diversification rates of primary colonizers. Models currently employed to test ecological opportunity do a poor job of explaining muroid diversity. In addition, the various rate-shift metrics identified different clades, suggesting that caution should be used when only one is applied, and we discuss which methods are most appropriate to address different questions of diversification.
To quantify the 'emptiness' of adaptive space a mathematical model of diversification is derived which makes explicit the relationship between maximum species capacity and realized diversity. The proportion of niches empty at equilibrium is a function only of the intrinsic rates of species origination and extinction. Estimates of these rates for 8 marine invertebrate groups suggest that the mean proportion of empty niches is somewhere in the range of 12-54%. Evolution in such an open adaptive space should be characterized by unremitting taxonomic turnover and continuous faunal change (but only occasional adaptive improvements), and should permit the rapid establishment of new morphospecies. These expectations are qualitatively borne out by the fossil record. -from Authors
Interspecific comparisons of phenotypes are used extensively to test hypotheses about the evolutionary forces shaping phenotypic variation, but comparative data analysis is complicated by correlations due to the common ancestry of species. The method of evolutionary contrasts removes such correlations by estimating the amount of character change between pairs of closely related species that has occurred since their most recent common ancestors. The original method allows character change to be estimated only along pairs of branches on a phylogeny, but many hypotheses address change along single branches. In this article the method of evolutionary contrasts is extended to allow character change along a set of single branches on a phylogeny to be estimated, expected variances are presented, and it is shown that these extensions also result in a set of contrasts that are not correlated because of common ancestry. These extensions will allow hypotheses to be tested concerning character change associated with host or habitat shifts, changes in breeding system (e.g., monogamy vs. polygyny, monoecy vs. dioecy), changes in life history (e.g., semelparity vs. iteroparity), and changes in quantitative characters in many other situations in which one is interested in character change along single branches.
Of the three southern continents, South America was more isolated during the Tertiary than Africa, less isolated than Australia. Its record of Cenozoic mammalian life is better than that of either. This record suggests that around the beginning of the Cenozoic, South America received a few wait immigrants-marsupials, edentates, ungulates-that reached the continent across a water barrier. The source area was probably Central America, which formed a tropical North American peninsula until near the end of Tertiary time. A few later wait immigrants reached the continent across the water barrier-rodents in the later part of the Eocene, primates then or in the early Oligocene, and procyonids perhaps late in the Miocene. From the descendants of these few immigrants a balanced fauna evolved that was strikingly different in composition from those of other continents. The evolution of the various groups composing it is briefly presented and discussed. At the end of the Tertiary the isolation of the continent ended ...
Two methods are discussed for assessing the contributions of subgroups to the morphological disparity of the larger group containing them. (1) Given an ordination of points representing specimens or species in morphological space, morphological disparity of the entire group is measured as the average squared distance of points from the centroid. (2) An alternative approach is to compare morphological disparity of a group to the disparity it would have if a certain subgroup were omitted. If the resulting disparity differs substantially from the original disparity, then the subgroup in question is considered to have a significant effect on morphological disparity. The two methods are applied to morphological disparity in trilobites, partitioned at different levels in the taxanomic hierarchy. Results of the two methods are intuitively reasonable and largely in agreement, and point to the predominance of Early Cambrian olenelloids, Cambro-Ordovician Libristoma, Ordovician Asaphina and Cheirurina, Siluro-Devonian Phacopida and Phacopina, and Devonian Proetida. -from Author
▪ Abstract The diversity of organismic form has evolved nonuniformly during the history of life. Quantitative morphological studies reveal profound changes in evolutionary rates corresponding with the generation of morphological disparity at low taxonomic diversity during the early radiation of many clades. These studies have also given insight into the relative importance of genomic and ecological factors in macroevolution, the selectivity of extinction, and other issues. Important progress has been made in the development of morphological spaces that can accommodate highly disparate forms, although this area still needs more attention. Other future directions include the relationship between morphological and ecological diversification, geographic patterns in morphological diversity, and the role of morphological disparity as a causal factor in macroevolution.
Force‐platform records and films of kangaroos and a wallaby hopping have been analysed to obtain data about the energetics of hopping and about the stresses which act in muscles, tendons and the tibia. The quantitative anatomical data required for the analysis have been obtained from X‐radiographs and dissections. It is shown that fluctuations of potential energy and external kinetic energy account for most of the energy cost of hopping; fluctuations of internal kinetic energy are relatively unimportant. Evidence is presented that large savings of energy are effected by elastic storage of energy in the gastrocnemius and plantaris tendons. The elastic mechanism is particularly effective at high speeds and seems to account for the observation of Dawson & Taylor (1973) that oxygen consumption is more or less constant over the whole range of hopping speeds. A mathematical model of hopping is presented. The stresses which occur in hopping are discussed.
Summary
Force platform records and films have been made of kangaroos and a wallaby hopping.
The maximum forces exerted on the ground were about six times body weight. The force exerted on the ground changes direction, throughout the period when the feet are on the ground, so that it is always more or less in line with the centre of mass. Consequently the animal decelerates a little and then accelerates again, during the contact phase.
The fluctuations of potential energy which occur in each hop are slightly smaller at high speeds than at low ones. Fluctuations of external kinetic energy increase with speed and account for most of the energy cost of hopping at high speeds. Fluctuations of internal kinetic energy (due to acceleration and deceleration of the limbs) are relatively small. While the feet are on the ground the extensor muscles of the hip do positive work, those of the knee negative work and those of the ankle negative work followed by positive work. The energy cost of hopping is reduced substantially by elastic storage of energy in the Achilles tendon. In the case of a wallaby hopping at moderate speed the calculated saving was 40%. The maximum stresses developed in leg muscles, tendons and the tibia have been calculated and are discussed in relation to the known properties of muscle, tendon and bone. The trunk pitches as the animal hops because the two legs swing forwards and back simultaneously. Appropriate tail movements reduce, but do not eliminate, this effect. A mathematical theory of hopping is presented and used to investigate the merits of different hopping techniques.
Dawson & Taylor's (1973) discovery that the rate of oxygen consumption of kangaroos decreases a little, as hopping speed increases, is probably to be explained by the increased role of elastic storage of energy at high speeds.