Speciation Times Research Articles

Deep Time and Domestication in Vahni (Anthony Ezekiel) Capildeo’s ‘Dog or Wolf’

Abstract In this short article, I read Vahni (Anthony Ezekiel) Capildeo’s lyric poem ‘Dog or Wolf’ as an illustration of how a poem can encompass the deep time of co-evolution and speciation (the process whereby species diverge). According to Jonathan Culler, there is a “special now” of lyric poetry: we encounter any poem in a perpetual present, but one with an open temporal horizon. Drawing on Deborah Bird Rose’s concept of ethical time, I suggest that the “gentle howling” of Capildeo’s ambiguous canid, which echoes Rose’s suggestion that other species call us into being, shows how poetry can also be a means of marking very deep time.

Estimation of speciation times under the multispecies coalescent.

The multispecies coalescent model is now widely accepted as an effective model for incorporating variation in the evolutionary histories of individual genes into methods for phylogenetic inference from genome-scale data. However, because model-based analysis under the coalescent can be computationally expensive for large datasets, a variety of inferential frameworks and corresponding algorithms have been proposed for estimation of species-level phylogenies and associated parameters, including speciation times and effective population sizes. We consider the problem of estimating the timing of speciation events along a phylogeny in a coalescent framework. We propose a maximum a posteriori estimator based on composite likelihood (MAPCL) for inferring these speciation times under a model of DNA sequence evolution for which exact site-pattern probabilities can be computed under the assumption of a constant θ throughout the species tree. We demonstrate that the MAPCL estimates are statistically consistent and asymptotically normally distributed, and we show how this result can be used to estimate their asymptotic variance. We also provide a more computationally efficient estimator of the asymptotic variance based on the non-parametric bootstrap. We evaluate the performance of our method using simulation and by application to an empirical dataset for gibbons. The method has been implemented in the PAUP* program, freely available at https://paup.phylosolutions.com for Macintosh, Windows and Linux operating systems. Supplementary data are available at Bioinformatics online.

Spatially explicit phylogeographical reconstruction sheds light on the history of the forest cover in the Congo Basin

AbstractAimThe impact of Pleistocene climatic oscillations on the biodiversity of African tropical rain forests remains poorly understood, and the Congo Basin is particularly understudied. We aim to elucidate how Pleistocene climatic oscillations shaped lowland tropical rain forests by investigating the intraspecific diversity and evolutionary history of a widespread tree species.LocationGuineo‐Congolian rain forest, Central Africa.TaxonStaudtia kamerunensis Warb. (Myristicaceae).MethodsWe used genome skimming combined with maximum likelihood and Bayesian inference to infer the plastid phylogeny. We estimated the time of speciation and differentiation, genetic diversity, and we employed a continuous phylogeographical approach to infer the dispersal history of its plastid lineages.ResultsWe sequenced an average of 5,827,783 reads per sample, and the reconstructed reference plastome had a mean depth of 73.3. We identified five plastid lineages that diverged during the Early or Middle Pleistocene and are parapatric, suggesting past population fragmentation. Four lineages are endemic to Lower Guinea, and one spans the Congo Basin. We found contrasting patterns of expansion in the two regions, with a rapid and recent range expansion of the Congolian lineage in the last 200,000 years, while the spread of the Lower Guinean lineages was substantially slower.Main conclusionThe contrasting demographic histories between eastern and western lineages, associated with contrasted levels of plant species richness and rates of endemism, suggest that forest cover was more stable in Lower Guinea during the Late Pleistocene than in Congolia, where the biodiversity might have been eroded before the forest re‐expanded in the Congo basin. This study illustrates how a continuous phylogeographical inference approach, mostly applied so far for inferring the spread of fast‐evolving pathogens over months or years, can provide new insights to reconstruct the dispersal history of tropical tree species over thousands or millions of years.

Genomic analyses of rice bean landraces reveal adaptation and yield related loci to accelerate breeding

Rice bean (Vigna umbellata) is an underexploited domesticated legume crop consumed for dietary protein in Asia, yet little is known about the genetic diversity of this species. Here, we present a high-quality reference genome for a rice bean landrace (FF25) built using PacBio long-read data and a Hi-C chromatin interaction map, and assess the phylogenetic position and speciation time of rice bean within the Vigna genus. We sequence 440 landraces (two core collections), and GWAS based on data for growth sites at three widely divergent latitudes reveal loci associated with flowering and yield. Loci harboring orthologs of FUL (FRUITFULL), FT (FLOWERING LOCUS T), and PRR3 (PSEUDO-RESPONSE REGULATOR 3) contribute to the adaptation of rice bean from its low latitude center of origin towards higher latitudes, and the landraces which pyramid early-flowering alleles for these loci display maximally short flowering times. We also demonstrate that copy-number-variation for VumCYP78A6 can regulate seed-yield traits. Intriguingly, 32 landraces collected from a mountainous region in South-Central China harbor a recently acquired InDel in TFL1 (TERMINAL FLOWER1) affecting stem determinacy; these materials also have exceptionally high values for multiple human-desired traits and could therefore substantially advance breeding efforts to improve rice bean.

Understanding the relationship between dispersal and range size.

The drivers of variability in species range sizes remain an outstanding enigma in ecology. The theoretical expectation of a positive dispersal-range size relationship has received mixed empirical support, despite dispersal being one of the most prominent hypothesised predictors of range size. Here, we synthesised results from 86 studies examining the dispersal-range size relationship for plants and animals in marine, terrestrial and freshwater realms. Overall, our meta-analysis showed that dispersal positively affects range size, but its effect is dependent on the clade and dispersal proxy studied. Moreover, despite potential differences in habitat connectivity, we did not find an effect of realm on the dispersal-range size relationship. Finally, the strength of the dispersal-range size relationship was dependent on latitude, range size metric and the taxonomic breadth of the study clade. Our synthesis emphasizes the importance of developing a mechanistic understanding of the trait to dispersal to range size relationship, considering the complexity of dispersal departure, transfer and settlement, as well as evolutionary components such as time for range expansion, speciation and past geological-environmental dynamics. We, therefore, call for a more integrative view of the dispersal process and its causal relationship with range size.

Time for speciation and niche conservatism explain the latitudinal diversity gradient in clupeiform fishes

AbstractAimThe latitudinal diversity gradient of increasing species richness from poles to equator is one of the most striking and pervasive spatial patterns of biodiversity. Climate appears to have been key to the formation of the latitudinal diversity gradient, but the processes through which climate shaped species richness remain unclear. We tested predictions of the time for speciation, carrying capacity and diversification rate latitudinal diversity gradient hypotheses in a trans‐marine/freshwater clade of fishes.LocationGlobal in marine and freshwater environments.TaxonClupeiformes (anchovies, herrings, sardines and relatives).MethodsWe tested predictions of latitudinal diversity gradient hypotheses using a molecular phylogeny, species distribution data and phylogenetic comparative approaches. To test the time for speciation hypothesis, we conducted ancestral state reconstructions to infer the ages of temperate, subtropical and tropical lineages and frequency of evolutionary transitions between climates. We tested the carry capacity hypothesis by characterizing changes in net diversification rates through time. To test the diversification rate hypothesis, we qualitatively compared the diversification rates of temperate, subtropical and tropical lineages and conducted statistical tests for associations between latitude and diversification rates.ResultsWe identified four transitions to temperate climates and two transitions out of temperate climates. We found no differences in diversification rates among temperate and tropical clupeiforms. Net diversification rates remained positive in crown Clupeiformes since their origin ~150 Ma in both tropical and temperate lineages. Climate niche characters exhibited strong phylogenetic signal. All temperate clupeiform lineages arose <50 Ma, after the Early Eocene Climatic Optimum.Main conclusionsOur results support the time for speciation hypothesis, which proposes that climate niche conservatism and fluctuations in the extent of temperate climates limited the time for species to accumulate in temperate climates, resulting in the latitudinal diversity gradient. We found no support for the carrying capacity or diversification rate hypotheses.

A draft genome of Drung cattle reveals clues to its chromosomal fusion and environmental adaptation

Drung cattle (Bos frontalis) have 58 chromosomes, differing from the Bos taurus 2n = 60 karyotype. To date, its origin and evolution history have not been proven conclusively, and the mechanisms of chromosome fusion and environmental adaptation have not been clearly elucidated. Here, we assembled a high integrity and good contiguity genome of Drung cattle with 13.7-fold contig N50 and 4.1-fold scaffold N50 improvements over the recently published Indian mithun assembly, respectively. Speciation time estimation and phylogenetic analysis showed that Drung cattle diverged from Bos taurus into an independent evolutionary clade. Sequence evidence of centromere regions provides clues to the breakpoints in BTA2 and BTA28 centromere satellites. We furthermore integrated a circulation and contraction-related biological process involving 43 evolutionary genes that participated in pathways associated with the evolution of the cardiovascular system. These findings may have important implications for understanding the molecular mechanisms of chromosome fusion, alpine valleys adaptability and cardiovascular function.

Comparative Analysis of Chloroplast Genomes of Seven Chaetoceros Species Revealed Variation Hotspots and Speciation Time.

Chaetoceros is a species-rich diatom genus with broad distribution and plays an important role in global carbon cycle and aquatic ecosystems. However, genomic information of Chaetoceros species is limited, hindering advanced researches on Chaetoceros biodiversity and their differential impact on ecology. In this study, we constructed full-length chloroplast genomes (cpDNAs) for seven Chaetoceros species, including C. costatus, C. curvisetus, C. laevisporus, C. muelleri, C. pseudo-curvisetus, C. socialis, and C. tenuissimus. All of these cpDNAs displayed a typical quadripartite structure with conserved genome arrangement and specific divergence. The sizes of these cpDNAs were similar, ranging from 116,421 to 119,034 bp in size, and these cpDNAs also displayed similar GC content, ranging from 30.26 to 32.10%. Despite extensive synteny conservation, discrete regions showed high variations. Divergence time estimation revealed that the common ancestor of Chaetoceros species, which formed a monophyletic clade at approximately 58 million years ago (Mya), split from Acanthoceras zachariasii at about 70 Mya. The availability of cpDNAs of multiple Chaetoceros species provided valuable reference sequences for studying evolutionary relationship among Chaetoceros species, as well as between Chaetoceros species and other diatom species.

The origin of an extreme case of sister‐species sympatry in a palm‐pollinator mutualistic system

AbstractAimMutualistic systems involving plants and brood pollinators show intriguing cases where a single plant is pollinated by several closely related sympatric species. This study aims at identifying the mechanisms involved in such an extreme case, where 10 sympatric weevil species are only associated with African oil palm inflorescences. We assessed the patterns and timing of speciation of this peculiar assemblage to explore the main drivers of its diversification.LocationTropical Africa.TaxonThe African oil palm Elaeis guineensis Jacquin (Arecaceae, Cocoseae), weevil genera Elaeidobius Kuschel and Prosoestus Faust (Curculionidae, Derelomini).MethodsWe first reassessed the status of the weevil species assemblage associated with the African oil palm based on a range of molecular species delimitation analyses. Second, we reconstructed a dated molecular phylogeny using Bayesian inference and maximum likelihood and carried out historical biogeographical analyses accounting for the main biogeographical barriers in tropical Africa.ResultsOur analyses generally confirm the validity of the species associated with the African oil palm and indicate that they form a monophyletic group. Dating analyses indicate that they originated about 7–8 million years ago (Mya) and that most speciation events occurred during the Pliocene and Pleistocene. Historical biogeography analyses reveal that one geographical barrier played a bigger role during their diversification. Age estimates suggest that extant weevil species remained in sympatry along the range of their host during the last 0.2 Mya.Main conclusionsThis case represents a remarkable example of a speciose mutualistic monophyletic insect assemblage. Our results indicate that past climatic oscillations in Western and Central Africa – where cycles of range contractions and expansions of the host drove the divergence of the weevils in allopatry – and the predominant role of a mountain range were instrumental in the emergence of the sympatric assemblage.

Comparative analysis of full-length mitochondrial genomes of five Skeletonema species reveals conserved genome organization and recent speciation

BackgroundSkeletonema species are prominent primary producers, some of which can also cause massive harmful algal blooms (HABs) in coastal waters under specific environmental conditions. Nevertheless, genomic information of Skeletonema species is currently limited, hindering advanced research on their role as primary producers and as HAB species. Mitochondrial genome (mtDNA) has been extensively used as “super barcode” in the phylogenetic analyses and comparative genomic analyses. However, of the 21 accepted Skeletonema species, full-length mtDNAs are currently available only for a single species, S. marinoi.ResultsIn this study, we constructed full-length mtDNAs for six strains of five Skeletonema species, including S. marinoi, S. tropicum, S. grevillei, S. pseudocostatum and S. costatum (with two strains), which were isolated from coastal waters in China. The mtDNAs of all of these Skeletonema species were compact with short intergenic regions, no introns, and no repeat regions. Comparative analyses of these Skeletonema mtDNAs revealed high conservation, with a few discrete regions of high variations, some of which could be used as molecular markers for distinguishing Skeletonema species and for tracking the biogeographic distribution of these species with high resolution and specificity. We estimated divergence times among these Skeletonema species using 34 mtDNAs genes with fossil data as calibration point in PAML, which revealed that the Skeletonema species formed the independent clade diverging from Thalassiosira species approximately 48.30 Mya.ConclusionsThe availability of mtDNAs of five Skeletonema species provided valuable reference sequences for further evolutionary studies including speciation time estimation and comparative genomic analysis among diatom species. Divergent regions could be used as molecular markers for tracking different Skeletonema species in the fields of coastal regions.

Historical biogeography of the Gondwanan freshwater genus Boeckella (Crustacea): Timing and modes of speciation in the Southern Hemisphere

AbstractAimWe investigated evolutionary relationships and biogeographical patterns within the genus Boeckella to evaluate (1) whether its current widespread distribution in the Southern Hemisphere is due to recent long‐distance dispersal or long‐term diversification; and (2) the age and origin of sub‐Antarctic and Antarctic Boeckella species, with particular focus on the most widely distributed species: Boeckella poppei.LocationSouth America, sub‐Antarctic islands, maritime Antarctica, continental Antarctica and Australasia.MethodsTo reconstruct phylogenetic patterns of Boeckella, we used molecular sequence data collected from 12 regions and applied Bayesian and Maximum Likelihood analyses using multiple loci. We also estimated divergence times and reconstructed ancestral ranges using two different models of species evolution.ResultsPhylogenetic analyses and divergence time estimates suggested that Boeckella originated on the Gondwanan supercontinent and initially split into two main clades during the late Cretaceous (ca. 80 Ma). The first clade diversified in Australasia, and the second clade is currently distributed in South America, various sub‐Antarctic islands and Antarctica. Dispersal from South America to the Kerguelen and Crozet archipelagos occurred during the Eocene/Oligocene (B. vallentini) and in the late Pliocene (B. brevicaudata), while South Georgia and the maritime Antarctic were likely colonized during the late Pleistocene (B. poppei).Main conclusionsBoeckella has a Gondwanan origin, with further diversifications after the physical separation of the continental landmasses. Extant populations of Boeckella from the Scotia Arc islands and Antarctic Peninsula originated from South America during the Pleistocene, suggesting that original Antarctic Gondwanan lineages did not survive repeated glacial cycles during the Quaternary ice ages. A continuous decline in the species accumulation rate is apparent within the genus as the early Eocene, suggesting that Boeckella diversification may have decreased due to progressive cooling throughout the Cenozoic era.

Petrobactin, a siderophore produced by Alteromonas, mediates community iron acquisition in the global ocean

It is now widely accepted that siderophores play a role in marine iron biogeochemical cycling. However, the mechanisms by which siderophores affect the availability of iron from specific sources and the resulting significance of these processes on iron biogeochemical cycling as a whole have remained largely untested. In this study, we develop a model system for testing the effects of siderophore production on iron bioavailability using the marine copiotroph Alteromonas macleodii ATCC 27126. Through the generation of the knockout cell line ΔasbB::kmr, which lacks siderophore biosynthetic capabilities, we demonstrate that the production of the siderophore petrobactin enables the acquisition of iron from mineral sources and weaker iron-ligand complexes. Notably, the utilization of lithogenic iron, such as that from atmospheric dust, indicates a significant role for siderophores in the incorporation of new iron into marine systems. We have also detected petrobactin, a photoreactive siderophore, directly from seawater in the mid-latitudes of the North Pacific and have identified the biosynthetic pathway for petrobactin in bacterial metagenome-assembled genomes widely distributed across the global ocean. Together, these results improve our mechanistic understanding of the role of siderophore production in iron biogeochemical cycling in the marine environment wherein iron speciation, bioavailability, and residence time can be directly influenced by microbial activities.

Genome-wide investigation of the bZIP transcription factor gene family in Prunus mume: Classification, evolution, expression profile and low-temperature stress responses

Prunus mume is an important woody plant that has high ornamental and economic value, widely distributed and used in landscape architecture in East Asia. In plants, basic (region) leucine zipper (bZIP) transcription factors play important regulatory roles in growth, development, dormancy and abiotic stress. To date, bZIP transcription factors have not been systematically studied in P. mume. In this study, 49 bZIP genes were first identified in P. mume, and the PmbZIP family was divided into 12 groups according to the grouping principles for the Arabidopsis thaliana bZIP family. For the first time, we constructed a detailed model of the PmbZIP domains (R-x3N-x7-R/K-x2-K-x6-L-x6-L-x6-L). Phylogenetic and synteny analyses showed that PmbZIPs duplication events might have occurred during the large-scale genome duplication events. A relatively short time of speciation and the finding that 91.84% of the bZIP genes formed orthologous pairs between P. mume and Prunus armeniaca provided evidence of a close relationship. Gene expression patterns were analysed in different tissues and periods, indicating that PmbZIP genes with the same motifs exhibited similar expression patterns. The gene expression results showed that PmbZIP31/36/41 genes played a more prominent role in the response to freezing stress than cold stress. The expression level of almost all subset III genes was upregulated under freezing treatment, especially after cold exposure. We analysed the gene expression patterns of PmbZIP12/31/36/41/48 and their responses to low-temperature stress, which provided useful resources for future studies on the cold/freezing-tolerant molecular breeding of P. mume.

Divergence-time estimates for hominins provide insight into encephalization and body mass trends in human evolution.

Quantifying speciation times during human evolution is fundamental as it provides a timescale to test for the correlation between key evolutionary transitions and extrinsic factors such as climatic or environmental change. Here, we applied a total evidence dating approach to a hominin phylogeny to estimate divergence times under different topological hypotheses. The time-scaled phylogenies were subsequently used to perform ancestral state reconstructions of body mass and phylogenetic encephalization quotient (PEQ). Our divergence-time estimates are consistent with other recent studies that analysed extant species. We show that the origin of the genus Homo probably occurred between 4.30 and 2.56 million years ago. The ancestral state reconstructions show a general trend towards a smaller body mass before the emergence of Homo, followed by a trend towards a greater body mass. PEQ estimations display a general trend of gradual but accelerating encephalization evolution. The obtained results provide a rigorous temporal framework for human evolution.

Phylogeny and time scale of diversification in the fossil-rich sunfishes and black basses (Teleostei: Percomorpha: Centrarchidae)

Species of the North American freshwater fish lineage Centrarchidae are apex predators in their habitats and are among the world’s most popular sport fishes. Centrarchids boast a rich fossil record that extends from the latest Eocene to the Pleistocene. To investigate the phylogeny and timing of diversification of Centrarchidae, we deploy a dataset of DNA sequences of 16 nuclear genes sampled from nearly all of the recognized and undescribed species. We also utilize previously published morphological datasets to assess the phylogenetic placement of one of the oldest known centrarchid fossils, †Plioplarchus whitei. A Bayesian multispecies coalescent species tree analysis provides insight on relationships that evaded resolution in earlier studies, such as the relationships of Acantharchus pomotis, the resolution of a clade consisting of species previously synonymized under the Spotted Bass, Micropterus punctulatus, and a clade of recently described species previously considered populations of the Redeye Bass, Micropterus coosae. This new molecular phylogeny and the inclusion of †P. whitei and other centrarchid fossils in the tip-dated fossilized birth–death analysis results in a new hypothesis of the timing of diversification in Centrarchidae that contextualizes the ages of centrarchid fossils to the timing of speciation among the extant species. In addition to providing new temporal perspectives on the diversification of freshwater fishes in North America, this study may close of the chapter of centrarchid phylogeny inferred using Sanger-sequenced genes, as the use of genomic-scale datasets becomes mainstream in the phylogenetics of fishes.

Gulf Coast vicariance shapes phylogeographic history of a North American freshwater mussel species complex

AbstractAimFreshwater mussels share habitat and are parasites of freshwater fishes during the larval life stage. Therefore, models of fish biogeography may also explain the historical biogeography of freshwater mussels. We tested this assumption using predictions of three biogeographic models constructed for northern Gulf of Mexico drainages on a freshwater mussel species complex. Specifically, we tested (1) if speciation was due to vicariant events of fluctuating sea levels that separated lineages east‐west of the Mobile Basin (Central Gulf Coast speciation hypothesis), (2) if the timing of divergences occurred 8.5–3.5 MYA (Gulf Coast allopatric speciation model) and (3) if diversification in Mississippi River populations was recent and for evidence of population increase consistent with range expansion into northern deglaciated regions (Pleistocene glaciation model).LocationEastern North America.TaxonFreshwater mussels (Bivalvia: Unionidae), Lampsilis teres and L. floridensis.MethodsWe collected 249 specimens from 73 localities across the group's distribution. We used three molecular markers (COI, NDI & ITSI) to conduct time calibrated Bayesian phylogenetic analyses, phylogeographic analyses (AMOVA & SAMOVA) and demographic analyses including Bayesian skyline plots.ResultsLampsilis teres and L. floridensis are allopatric species whose distributions meet at the eastern edge of the Mobile Basin. Speciation was estimated to occur in the late Miocene. Populations from isolated river systems surrounding the Gulf of Mexico are almost all monophyletic. Mississippi drainage samples formed a shallow clade with recent diversification and showed evidence of recent population expansion.Main conclusionsThe historical biogeography of the L. teres species complex is broadly consistent with tested ichthyofaunal models. The timing of speciation and intraspecific divergences correspond to low sea‐level events suggesting that Gulf Coast sea‐level fluctuations are responsible for dispersal (sea‐level recession) and subsequent cladogenesis (sea‐level inundation). Consistent with numerous other freshwater studies, we found the Mobile Basin to be a suture zone, which may be due to the narrow, offshore continental shelf.

Genomic insights into the host specific adaptation of the Pneumocystis genus

Pneumocystis jirovecii, the fungal agent of human Pneumocystis pneumonia, is closely related to macaque Pneumocystis. Little is known about other Pneumocystis species in distantly related mammals, none of which are capable of establishing infection in humans. The molecular basis of host specificity in Pneumocystis remains unknown as experiments are limited due to an inability to culture any species in vitro. To explore Pneumocystis evolutionary adaptations, we have sequenced the genomes of species infecting macaques, rabbits, dogs and rats and compared them to available genomes of species infecting humans, mice and rats. Complete whole genome sequence data enables analysis and robust phylogeny, identification of important genetic features of the host adaptation, and estimation of speciation timing relative to the rise of their mammalian hosts. Our data reveals insights into the evolution of P. jirovecii, the sole member of the genus able to infect humans.

The geography of phylogenetic paleoecology: integrating data and methods to better understand biotic response to climate change

AbstractDeeper knowledge about how species and communities respond to climate change and environmental gradients should be supported by evidence from the past, especially as modern responses are influenced by anthropogenic pressures, including human population growth, habitat destruction and fragmentation, and intensifying land use. There have been great advances in modeling species’ geographic distributions over shallow time, where consideration of evolutionary change is likely less important due to shorter time for evolution and speciation to occur. Over these shallow time periods, we have more resources for paleoclimate interpretation across large geographic landscapes. We can also gain insight into species and community changes by studying deep records of temporal changes. However, modeling species geographic distributions in deep time remains challenging, because for many species there is sparse coverage of spatial and temporal occurrences and there are fewer paleoclimate general circulation models (GCMs) to help interpret the geographic distribution of climate availability. In addition, at deeper time periods, it is essential to consider evolutionary change within lineages of species. I will discuss a framework that integrates evolutionary information in the form of phylogenetic relatedness from clades of extant closely related species, where and when there are associated fossil occurrences, and the geographic distribution of paleoclimate in deep time to infer species past geographic response to climate change and to estimate where and when there were hotspots of ancient diversification. More work is needed to better understand the evolution of physiological tolerances and how physiological tolerances relate to the climate space in which species occur.

The effects of geographic range size and abundance on extinction during a time of “sluggish”’ evolution

AbstractGeographic range size and abundance are important determinants of extinction risk in fossil and extant taxa. However, the relationship between these variables and extinction risk has not been tested extensively during evolutionarily “quiescent” times of low extinction and speciation in the fossil record. Here we examine the influence of geographic range size and abundance on extinction risk during the late Paleozoic (Mississippian–Permian), a time of “sluggish” evolution when global rates of origination and extinction were roughly half those of other Paleozoic intervals. Analyses used spatiotemporal occurrences for 164 brachiopod species from the North American midcontinent. We found abundance to be a better predictor of extinction risk than measures of geographic range size. Moreover, species exhibited reductions in abundance before their extinction but did not display contractions in geographic range size. The weak relationship between geographic range size and extinction in this time and place may reflect the relative preponderance of larger-ranged taxa combined with the physiographic conditions of the region that allowed for easy habitat tracking that dampened both extinction and speciation. These conditions led to a prolonged period (19–25 Myr) during which standard macroevolutionary rules did not apply.

Modeling colonization rates over time: Generating null models and testing model adequacy in phylogenetic analyses of species assemblages.

A central theme connecting macroevolutionary processes to macroecological patterns is the shaping of regional biodiversity over time through speciation, extinction, migration, and range shifts. The use of phylogenies to explore the dynamics of diversification due to variation in speciation and extinction rates has been well-developed and there are established methods for inferring speciation times from phylogenies and generating its null distributions (as represented by node heights on molecular phylogenies). But inferring colonization events from phylogenies is more challenging. Unlike speciation events, represented by nodes, colonization events could occur at any point along a branch connecting species in the assemblage to the regional pool. We account for uncertainty in identification of colonization lineages and timing of colonization events by using an efficient analytical solution to inferring the distribution of colonization times from an assemblage phylogeny. Using the same solution, we efficiently derive the null distribution of colonization times, which provides us with a general approach to testing the adequacy of a model to describe colonization events into the assemblage. We illustrate this approach by demonstrating how the movement of squamate lineages into Madagascar has been uneven over time, peaking in the early Cenozoic when ocean conditions favored colonization.