ThesisPDF Available

Ecological diversification and biogeography in the Neogene: Evolution of a major lineage of American and Caribbean rodents (Caviomorpha, Octodontoidea)

Abstract and Figures

A major topic in evolutionary biology concerns the process of biological diversification. The cosmopolitan order Rodentia is the most diverse mammalian radiation with ca. 2300 living species, or about 40% of all mammals. The Caviomorpha, best known from the domesticated guinea pig (Cavia), was the first rodent lineage to reach South America. Their Eocene origin from Africa is supported by both molecular and paleontological data sets. Caviomorphs have since radiated to 244 modern species in the Americas and Caribbean, spanning three orders of magnitude in body size (i.e., ~60 g to ~60 kg). The superfamily Octodontoidea (186 species) collectively exploits most ecological niches used by rodents, from tree-dwelling to burrowing, rock-dwelling, terrestrial, and even semi-aquatic forms. Reconstructing the timing and patterns of this evolutionary diversification has been problematic, however, due to convergent morphologies, incomplete fossils, and sparse sampling of species in molecular phylogenies. The goals of this dissertation were to (i) establish a temporal and phylogenetic framework for this lineage consistent with fossil and molecular data, and (ii) use it to investigate ecological and geographic drivers of diversification over the last 23 million years (Neogene – Recent). Molecular phylogenetic analyses were conducted across all 54 living genera (and 68% of species) in Caviomorpha plus related rodents in Africa and Asia for two mitochondrial (cyt-b and 12S rRNA) and three nuclear genes (GHR, vWF, and RAG1). Clade divergence times were estimated using a relaxed molecular clock and 22 fossil calibrations. The timetree supports the divergence of Caviomorpha from Phiomorpha (Africa) in the Middle Eocene ~42 Ma, presumably via over-water dispersal to South America. That clade + African and Asian porcupines is strongly supported as crown Hystricognathi with an ~45 Ma age. Within Phiomorpha, the ~31 Ma divergence of the naked mole-rat (Heterocephalus) from all other mole-rats argues for recognition of this group as Bathyergoidea, containing the families Heterocephalidae and Bathyergidae. Within Caviomorpha, the four traditional superfamilies were recovered with ~32 Ma stem divergences as Cavioidea + Erethizontoidea and Chinchilloidea + Octodontoidea. Five families were united in Octodontoidea, with Abrocomidae (chinchilla rats) sister to two family dyads: Octodontidae (degus and viscacha rats) + Ctenomyidae (tuco-tucos) and Echimyidae (spiny rats, tree rats, and the nutria) + Capromyidae (hutias). Although the five genera of capromyids form a robustly monophyletic group, they were recovered as the uncertain sister to a group of Brazilian echimyids, possibly rendering Echimyidae paraphyletic. Processes of geographic diversification were reconstructed using the timetree, geographic ranges for extant caviomorphs, and regions of endemism. By the beginning of the Neogene, each main lineage of Octodontoidea had diverged from an ancestor most likely distributed in the Southern Andes/Patagonia. With the onset of more arid climates in southern South America ~18 Ma, the crown radiations of both family dyads had begun. Ensuing divergences in space and ecology resulted in a southern, arid-adapted clade (Octodontidae-Ctenomyidae, 76 species) and a northern, mesic-adapted clade (Echimyidae-Capromyidae, 102 species). Rates of species diversification were dramatically different among these clades, with a long stem leading to the last ~5 Ma of rapid radiation in Ctenomyidae, versus at least 18 lineages present by 10 Ma in Echimyidae-Capromyidae. The best-fitting processes for these patterns were positive diversity dependence (likely due to high species turnover) in Octodontidae-Ctenomyidae, and either decreasing diversity dependence or constant rates in Echimyidae-Capromyidae. The geo-climatic differentiation of northern and southern South America during the Neogene may have driven the disparate divergence processes for these rodent clades. The uplift of montane Andean habitats is implicated in both the aridification of southern climates and in the northern radiation of Echimyidae, with at least four transitions found in their phylogeny between the lowland Amazon and highland Andes. A survey of 86 other animal lineages reinforces that finding, and suggests that both directions of transition were common after ~7.5 Ma. Processes of ecological diversification were investigated to test for signatures of adaptive radiation throughout the timetree. Body masses and ecological life modes were mapped on the timetree for all species and used for modeling body-size disparification. Different evolutionary processes again characterized Octodontoidea’s northern and southern clades. In Ctenomyidae, rates of body-size disparification accelerated in step with species diversification, and in accord with their modern species’ 10-fold variation in body mass. In contrast, analyses of Echimyidae-Capromyidae showed initially high and then declining rates of disparification. Among reconstructed life modes, multi-optimum Ornstein-Uhlenbeck models were favored over constant rate (Brownian motion) models. Rodents in different life modes appear to occupy different regions of morphospace and, presumably, ecospace. Burrowing rodents were modeled as having a significantly smaller and less variable optimum size than tree-dwelling or terrestrial rodents, suggesting that subterranean living may impose size constraints. In the context of Simpson’s adaptive zones, Ctenomyidae is confined to the single zone of burrowing while Echimyidae-Capromyidae occupies at least two (burrowing and tree-dwelling). Hence, even though Ctenomyidae is both diverse and disparate it does not appear to constitute an adaptive radiation. Echimyidae-Capromyidae is a candidate for an old adaptive radiation that has persisted after saturating available niches. In both cases, greater integration of phylogenetic and geographic information from fossils is expected to improve our understanding of these radiations.
Content may be subject to copyright.
A preview of the PDF is not available
... However, Cavioidea (guinea pigs and capybaras) and Chinchilloidea (chinchillas and pacaranas) both formerly exhibited considerably greater diversity: each superfamily was represented by 20 genera during the Late Miocene (11.2-5.3 Ma), alongside 18 genera of octodontoids from the same time period (McKenna and Bell, 1997;Upham, 2014). Analyses of their diversity over time are, however, beyond the scope of this paper and are instead the subject of a succeeding one. ...
... Emmons and Vucetich (1998) recognized many differences in cranial characters between this form and other living echimyids and erected a new genus for it and a related fossil form. Recovery of Callistomys in lineage II with semi-aquatic Myocastor and the terrestrial spiny rats Proechimys + Hoplomys suggests that its soft fluffy pelage and arboreal or scansorial habits evolved independently from similar traits in lineage I (see also Upham, 2014;Loss et al., 2014). Resemblances between Callistomys and extinct echimyid lineages in the mid-Miocene and earlier (e.g., †Maruchito; Emmons and Vucetich, 1998; make it likely that the nearest relatives of Callistomys are missing from our phylogenetic tree. ...
... This poses a key question about the subsequent evolution of these clades: What factors led to the greater longevity of lineages in Echimyidae-Capromyidae (many Miocene-aged lineages) compared to those in Octodontidae-Ctenomyidae (two surviving lineages from the late Miocene)? The fact that the southern clade of octodontids and ctenomyids had to adapt to arid climates unprecedented in the Paleogene (Fig. 6.2), suggests one reason for the apparently greater turnover of species during the initial stages of their radiation ( Fig. 5; Upham, 2014). Spatiotemporal and ecomorphological data from the fossil record need to be reconciled with the region's progressive aridification, especially now that rates and sequences of lineage diversification can be inferred from the molecular timetree. ...
Chapter
Full-text available
The Caviomorpha is a diverse lineage of hystricognath rodents endemic to the Americas and Caribbean islands. We analyzed evolutionary relationships within 11 families of caviomorphs and their relatives in the suborder Ctenohystrica using a supermatrix of 199 taxa and DNA sequences from five genes. New gene sequences were generated for 33 genera, including 12 genera newly available for molecular analysis. Presented here are the analyses pruned to a single representative for each genus, totaling 68 of the 70 living genera in Ctenohystrica. Our analyses recovered strong support for Hystricognathi containing the monophyletic groups Hystricidae, Phiomorpha, and Caviomorpha, with the latter two groups as well- supported sister taxa. The analyses also strongly supported the monophyly of the four traditional superfamilies of caviomorphs, with Cavioidea + Erethizontoidea and Chinchilloidea (including Dinomyidae) + Octodontoidea. Cuniculidae + Dasyproctidae are recovered as sister to Caviidae (including Hydrochoerus). Abrocomidae (including Cuscomys) is sister to the remaining octodontoid families, consisting of the dyads Octodontidae + Ctenomyidae and Echimyidae (including Myocastor) + Capromyidae. The five genera of capromyids form a robustly monophyletic group, but they are allied to a group of Brazilian echimyids, rendering Echimyidae paraphyletic. We dated nodes in our tree by comparing eight sets of fossil calibrations, identifying a set of 22 calibrations that minimized internal age conflicts.The resulting timetree dates the Hystricognathi crown to the Middle Eocene, 44.9 Ma, and the phiomorph-caviomorph split to 42.0 Ma. Crown caviomorphs diverged at 35.7 Ma, and splits of Cavioidea-Erethizontoidea and Chinchilloidea-Octodontoidea occurred at 32.4 Ma and 32.8 Ma, respectively. Most families appeared in the late Oligocene-Early Miocene and virtually all genera are of Middle-Late Miocene age, with a few exceptions. We briefly consider geo-climatic changes that might have influenced the evolution of hystricognath rodents, deferring to another work a detailed analysis of their rates and ecological drivers of diversification.
... Quantitative evidence of body mass variations in hystrico-and sciuromorphs is overwhelming 1,[123][124][125] . We showed that the rate of body mass evolution was higher in the ancestral hystricomorph and sciuromorph, which coincided with the ancestral nature of the 3p21.31 ...
Article
Full-text available
The rodents of hystricomorpha and sciuromorpha suborders exhibit remarkably lower incidence of cancer. The underlying genetic basis remains obscure. We report a convergent evolutionary split of human 3p21.31, a locus hosting a large number of tumour-suppressor genes (TSGs) and frequently deleted in several tumour types, in hystrico- and sciuromorphs. Analysis of 34 vertebrate genomes revealed that the synteny of 3p21.31 cluster is functionally and evolutionarily constrained in most placental mammals, but exhibit large genomic interruptions independently in hystricomorphs and sciuromorphs, owing to relaxation of underlying constraints. Hystrico- and sciuromorphs, therefore, escape from pro-tumorigenic co-deletion of several TSGs in cis. The split 3p21.31 sub-clusters gained proximity to proto-oncogene clusters from elsewhere, which might further nullify pro-tumorigenic impact of copy number variations due to co-deletion or co-amplification of genes with opposing effects. The split of 3p21.31 locus coincided with the accelerated rate of its gene expression and the body mass evolution of ancestral hystrico- and sciuromorphs. The genes near breakpoints were associated with the traits specific to hystrico- and sciuromorphs, implying adaptive significance. We conclude that the convergently evolved chromosomal interruptions of evolutionarily constrained 3p21.31 cluster might have impacted evolution of cancer resistance, body mass variation and ecological adaptations in hystrico- and sciuromorphs.
... Climatic oscillations of the Pleistocene have been overwhelmingly important to mammalian diversification, as shown by molecular phylogenies for many groups: e.g., Carollia perspicillata (Pavan et al. 2011); Brazilian Alouatta ; Pteronotus parnellii (Clare et al. 2013); and various Lycalopex species (Tchaicka et al. 2016). Nevertheless, time-trees show that many speciation events predated the Pleistocene (e.g., Upham 2014), and at least some paleoclimatic reconstructions suggest that forests weren't hugely reshuffled during glacial cycles (Colinvaux 2007). Pleistocene glacial episodes also emptied oceans, exposing continental shelves and facilitating island colonization. ...
... Body size patterns have been explored for a few rodent groups (e.g., Medina et al. 2007;Maestri et al. 2016). Body size variation in caviomorphs is very heterogeneous in its rates of evolution (Álvarez et al. 2017) and seems to be associated with variation in life mode (Upham 2014), although we still lack a clear picture of how size is spatially distributed. For sigmodontines, assemblages of species with larger body sizes seem to be associated with open and warm areas in South America , but more studies are needed to refine body size estimates and investigate within-species and cross-species patterns. ...
... Two species initially assigned to Mysatelesgundlachi and meridionalis on Isla de la Juventud, the largest off-Cuba island-are now interpreted as subspecies of prehensilis based on molecular and cranial data (Woods et al. 2001;Borroto-Páez et al. 2005;Silva Taboada et al. 2007). Mysateles melanurus was re-assigned to Mesocapromys following its inclusion in that genus in phylogenetic analyses of cytochrome-b (cytb- Woods et al. 2001;Borroto-Páez et al. 2005;Kilpatrick et al. 2012), a finding corroborated in multi-gene analyses (Upham 2014). A 5th taxon, garridoi, allocated to either Mysateles or Capromys was described from a single mummified specimen with particularly distinctive fecal pellets (Garrido 1971). ...
Article
Full-text available
The insular radiation of hutias is remarkable among mammals for its high rate of extinction during the Holocene (~58% of species), yet fragments of intact habitat throughout the West Indies retain a critical portion of endemic diversity needing assessment. Cuba contains 8 of the 11 recognized living species of hutias, with surviving forms also on Hispaniola, Jamaica, and the Bahamas. Herein, we performed molecular phylogenetic analyses across populations of Cuban hutias in the genera Capromys, Mesocapromys, and Mysateles to address major gaps in our understanding of their species limits, phylogenetic structure, and geographic distributions. Comparing sequences of mitochondrial genes (cyt-b, COI, 12S rRNA) from 41 individuals and 21 sites across the archipelago, we found evidence that Capromys pilorides contains a major species-level subdivision from western to eastern Cuba, spanning a greater geographic region than previously hypothesized. Populations of Capromys in each clade last shared a common ancestor ~1.1 million years ago (Ma; 5.2% cyt-b divergence). The western clade is further subdivided between mainland hutias (C. p. pilorides) and those on Isla de la Juventud plus Cayo Cantiles (C. p. relictus has priority). The eastern clade contains all Capromys east of Sierra del Escambray in central Cuba, including mainland and insular forms. However, without paired analyses of morphology and genetics or data from type localities, we cannot assign a name to the eastern Capromys sp. nov. at this time. Divergence- time analyses across 9 named species of hutias (plus 1 extinct), including nuclear genes (GHR, vWF, RAG1), dates the Capromyidae split from their South American relatives (Echimyidae) at 15.5 Ma. The crown radiation of hutias was 8.8 Ma, with successive divergences at 5.4 Ma (Geocapromys), 3.1 Ma (Capromys), and 2.2 Ma (Mysateles–Mesocapromys). Detailed surveys are needed to assess the conservation status of these evolutionarily distinct Cuban taxa.
... Future studies might therefore incorporate a richer species sampling within Thrichomys (five species are recognized) and Isothrix (six species are recognized), but, to our knowledge, the branch leading to Diplomys labilis could only be subdivided by adding D. caniceps, whereas Santamartamys rufodorsalis is monotypic. It is noteworthy that the analysis of Upham (2014) and Upham and Patterson (2015), based on ca. 5000 nucleotides but with enhanced taxon sampling (e.g., all 6 Isothrix), recovered stronger support for some of these same groupings (nodes M and R), but not others (nodes F and U). ...
Article
Full-text available
Echimyidae is one of the most speciose and ecologically diverse rodent families in the world, occupying a wide range of habitats in the Neotropics. However, a resolved phylogeny at the genus-level is still lacking for these 22 genera of South American spiny rats, including the coypu (Myocastorinae), and 5 genera of West Indian hutias (Capromyidae) relatives. Here we used Illumina shotgun sequencing to assemble 38 new complete mitogenomes, establishing Echimyidae, and Capromyidae as the first major rodent families to be completely sequenced at the genus-level for their mitochondrial DNA. Combining mitogenomes and nuclear exons, we inferred a robust phylogenetic framework that reveals several newly supported nodes as well as the tempo of the higher-level diversification of these rodents. Incorporating the full generic diversity of extant echimyids leads us to propose a new higher-level classification of two subfamilies: Euryzygomatomyinae and Echimyinae. Of note, the enigmatic Carterodon displays fast-evolving mitochondrial and nuclear sequences, with a long branch that destabilizes the deepest divergences of the echimyid tree, thereby challenging the sister-group relationship between Capromyidae and Euryzygomatomyinae. Biogeographical analyses involving higher-level taxa show that several vicariant and dispersal events impacted the evolutionary history of echimyids. The diversification history of Echimyidae seems to have been influenced by two major historical factors, namely (1) recurrent connections between Atlantic and Amazonian Forests and (2) the Northern uplift of the Andes.
Article
Full-text available
Reconstructing the tempo at which biodiversity arose is a fundamental goal of evolutionary biologists, yet the relative merits of evolutionary-rate estimates are debated based on whether they are derived from the fossil record or time-calibrated phylogenies (timetrees) of living species. Extinct lineages unsampled in timetrees are known to “pull” speciation rates downward, but the temporal scale at which this bias matters is unclear. To investigate this problem, we compare mammalian diversification-rate signatures in a credible set of molecular timetrees (n = 5,911 species, ∼70% from DNA) to those in fossil genus durations (n = 5,320). We use fossil extinction rates to correct or “push” the timetree-based (pulled) speciation-rate estimates, finding a surge of speciation during the Paleocene (∼66–56 million years ago, Ma) between the Cretaceous-Paleogene (K-Pg) boundary and the Paleocene-Eocene Thermal Maximum (PETM). However, about two-thirds of the K-Pg-to-PETM originating taxa did not leave modern descendants, indicating that this rate signature is likely undetectable from extant lineages alone. For groups without substantial fossil records, thankfully all is not lost. Pushed and pulled speciation rates converge starting ∼10 Ma and are equal at the present day when recent evolutionary processes can be estimated without bias using species-specific “tip” rates of speciation. Clade-wide moments of tip rates also enable enriched inference, as the skewness of tip rates is shown to approximate a clade’s extent of past diversification-rate shifts. Molecular timetrees need fossil-correction to address deep-time questions, but they are sufficient for shallower time questions where extinctions are fewer.
Article
Full-text available
[revised from pre-print posted on Current Biology's SSRN server: https://papers.ssrn.com/sol3/papers.cfm?abstract_id=3761886] Reconstructing the tempo at which biodiversity arose is a fundamental goal of evolutionary biologists, yet the relative merits of evolutionary-rate estimates are debated based on whether they are derived from the fossil record or time-calibrated phylogenies (timetrees) of living species. Extinct lineages unsampled in timetrees are known to ‘pull’ speciation rates downward, but the temporal scale at which this bias matters is unclear. To investigate this problem, we compare mammalian diversification-rate signatures in a credible set of molecular timetrees (N=5,911 species, ca. 70% from DNA) to those in fossil genus durations (N=5,320). We use fossil extinction rates to correct or ‘push’ the timetree-based (pulled) speciation-rate estimates, finding a major pulse of speciation ca. 66-56 million years ago (Ma) between the Cretaceous-Paleogene (K-Pg) boundary and the Paleocene-Eocene Thermal Maximum (PETM). However, three-quarters of the K-Pg-to-PETM originating taxa did not leave modern descendants, indicating that this rate signature is realistically not detectable from extant lineages alone. For groups without substantial fossil records, thankfully all is not lost. Pushed and pulled speciation rates converge starting ca. 10 Ma, and are equal at the present-day when recent evolutionary processes can be estimated without bias using species-specific ‘tip’ rates of speciation. Clade-wide moments of tip rates also enable enriched inference, as the skewness of tip rates is shown to approximate a clade’s extent of past diversification-rate shifts. Molecular timetrees need fossil-correction to address deep-time questions, but they are sufficient for shallower time questions where extinctions are fewer.
Article
Full-text available
The structure of the living Patagonian flora, dominated by the steppe, is a direct consequence of past climatic and tectonic events. These arid-adapted communities were widespread during the Late Neogene, but their origin in Patagonia can be traced back to the Paleogene. Vegetational trends throughout Paleocene-Miocene time are based on available paleobotanical and palynological information. Four major supported stages in vegetation turnovers are recognized: (1) Paleocene and Early Eocene floras were rainforest-dominated, including many angiosperms with warm-temperate affinities (e.g., palms, Juglandaceae, Casuarinaceae). However, mainly in the Early Eocene, some geographic areas influenced by warm but drier conditions are suggested by the occurrence of certain taxa (e.g., Anacardiaceae). These areas containing arid-adapted floras would have arisen in Patagonian inland regions, in a generally wet continent. (2) The Middle Eocene-Early Oligocene interval was distinguished by the invasion ofNothofagus forests. Progressive replacements of megathermal communities by meso- and microthermal rainforest are documented.Nothofagus forest expansion suggests a marked cooling trend at this time, although some megathermal elements (AquifoliaceaeIlex, Tiliaceae-Bombacaceae, Sapindaceae) were still present at the beginning of this period. Arid-loving taxa have not been recorded in abundance. (3) Late Oligocene-Early Miocene floras were characterized by the occurrence of shrubby-herbaceous elements belonging to Asteraceae, Chenopodiaceae, Ephedraceae, Convolvulaceae, Fabaceae, and Poaceae. They began to give a modern appearance to plant communities. Xerophytic formations would have occupied coastal salt marshes and pockets in inland areas. Megathermal angiosperms of the Rubiaceae, Combretaceae, Sapindaceae, Chloranthaceae, and Arecaceae occurred mainly during the Late Oligocene. Forests of Nothofagaceae, Podocarpaceae, and Araucariaceae are still documented in extra-Andean Patagonia; however, a contrast between coastal and inland environments may have developed, particularly in the Miocene. (4) Middle-Late Miocene records show an increasing diversity and abundance of xerophytic-adapted taxa, including Asteraceae, Chenopodiaceae, and ConvolvulaceaeCressa/Wilsonia. Expansion of these xerophytic taxa, coupled with extinctions of megathermal/nonseasonal elements, would have been associated with both tectonic and climatic forcing factors, led to the development of aridity and extreme seasonality. These arid-adapted Late Miocene floras are closely related to modern communities, with steppe widespread across extra-Andean Patagonia and forest restricted to the western humid upland regions.
Article
Forty-nine complete 12S ribosomal RNA (rRNA) gene sequences from a diverse assortment of mammals (one monotreme, 11 marsupials, 37 placentals), including 11 new sequences, were employed to establish a “core” secondary structure model for mammalian 12S rRNA. Base-pairing interactions were assessed according to the criteria of potential base-pairing as well as evidence for base-pairing in the form of compensatory mutations. In cases where compensatory evidence was not available among mammalian sequences, we evaluated evidence among other vertebrate 12S rRNAs. Our results suggest a core model for secondary structure in mammalian 12S rRNAs with deletions as well as additions to the Gutell (1994:Nucleic Acids Res. 22) models forBos andHomo. In all, we recognize 40 stems, 34 of which are supported by at least some compensatory evidence within Mammalia. We also investigated the occurrence and conservation in mammalian 12S rRNAs of nucleotide positions that are known to participate in the decoding site inE. coli. Twenty-four nucleotide positions known to participate in the decoding site inE. coli also occur among mammalian 12S rRNAs and 17 are invariant for the same base as inE. coli. Patterns of nucleotide substitution were assessed based on our secondary structure model. Transitions in loops become saturated by approximately 10–20 million years. Transitions in stems, in turn, show partial saturation at 20 million years but divergence continues to increase beyond 100 million years. Transversions accumulate lin early beyond 100 million years in both stems and loops although the rate of accumulation of transversions is three- to fourfold higher in loops. Presumably, this difference results from constraints to maintain pairing in stems.
Chapter
Molecular data provide several key insights into the origin and diversification of the Hawaiian lobeliads, which comprise one-ninth of the flora of the most isolated archipelago on earth. Soon after colonizing the Hawaiian chain from elsewhere in the Southern hemisphere, this group radiated into four major clades, adapted to bogs and other open, wet high-elevation habitats, to inland outcrops and rock walls, to sea cliffs and dry forest, and to rain- and cloud-forest edges and interiors. Woodiness and bird pollination arose long before the lobeliads arrived in Hawaii; fleshy fruits evolved autochthonously in moist to wet forests, and were lost on sea cliffs. Limited seed dispersal (associated with fleshy fruits in forest-interior plants) appears to have triggered substantial speciation in the genus Cyanea, and helped generate convergent radiations in flower length, elevational distribution, and plant height on each of the four major islands. Some of the processes that accelerated speciation in Cyanea —such as limited seed dispersal, narrow ranges, and highly specialized flowers — also appear to have increased the likelihood of extinction. The roles of adaptive radiation vis-à-vis limited dispersal and sexual selection in promoting speciation in other groups (African rift-lake cichlids, coral reef fish, lilies and their relatives) are also discussed, with special reference to the phenomena of convergent adaptive radiations and of visual selection. Natural enemies may exert stronger density-dependent mortality on their hosts under rainier, more humid, warmer, and less seasonal conditions, and help create strong ecological gradients in plant species diversity within the tropics. Adaptive radiation may thus have interacted synergistically with several processes to generate the taxonomic richness and ecological diversity of the largest clade in the Hawaiian flora.
Article
Phylogenies reconstructed from gene sequences can be used to investigate the tempo and mode of species diversification. Here we develop and use new statistical methods to infer past patterns of speciation and extinction from molecular phylogenies. Specifically, we test the null hypothesis that per-lineage speciation and extinction rates have remained constant through time. Rejection of this hypothesis may provide evidence for evolutionary events such as adaptive radiations or key adaptations. In contrast to previous approaches, our methods are robust to incomplete taxon sampling and are conservative with respect to extinction. Using simulation we investigate, first, the adverse effects of failing to take incomplete sampling into account and, second, the power and reliability of our tests. When applied to published phylogenies our tests suggest that, in some cases, speciation rates have decreased through time.