Speciation Times Research Articles

Estimating hybridization in the presence of coalescence using phylogenetic intraspecific sampling

BackgroundA well-known characteristic of multi-locus data is that each locus has its own phylogenetic history which may differ substantially from the overall phylogenetic history of the species. Although the possibility that this arises through incomplete lineage sorting is often incorporated in models for the species-level phylogeny, it is much less common for hybridization to also be formally included in such models.ResultsWe have modified the evolutionary model of Meng and Kubatko (2009) to incorporate intraspecific sampling of multiple individuals for estimation of speciation times and times of hybridization events for testing for hybridization in the presence of incomplete lineage sorting. We have also utilized a more efficient algorithm for obtaining our estimates. Using simulations, we demonstrate that our approach performs well under conditions motivated by an empirical data set for Sistrurus rattlesnakes where putative hybridization has occurred. We further demonstrate that the method is able to accurately detect the signature of hybridization in the data, while this signal may be obscured when other species-tree inference methods that ignore hybridization are used.ConclusionsOur approach is shown to be powerful in detecting hybridization when it is present. When applied to the Sistrurus data, we find no evidence of hybridization; instead, it appears that putative hybrid snakes in Missouri are most likely pure S. catenatus tergeminus in origin, which has significant conservation implications.

Time and Origin of Cichlid Colonization of the Lower Congo Rapids

Most freshwater diversity is arguably located in networks of rivers and streams, but, in contrast to lacustrine systems riverine radiations, are largely understudied. The extensive rapids of the lower Congo River is one of the few river stretches inhabited by a locally endemic cichlid species flock as well as several species pairs, for which we provide evidence that they have radiated in situ. We use more that 2,000 AFLP markers as well as multilocus sequence datasets to reconstruct their origin, phylogenetic history, as well as the timing of colonization and speciation of two Lower Congo cichlid genera, Steatocranus and Nanochromis. Based on a representative taxon sampling and well resolved phylogenetic hypotheses we demonstrate that a high level of riverine diversity originated in the lower Congo within about 5 mya, which is concordant with age estimates for the hydrological origin of the modern lower Congo River. A spatial genetic structure is present in all widely distributed lineages corresponding to a trisection of the lower Congo River into major biogeographic areas, each with locally endemic species assemblages. With the present study, we provide a phylogenetic framework for a complex system that may serve as a link between African riverine cichlid diversity and the megadiverse cichlid radiations of the East African lakes. Beyond this we give for the first time a biologically estimated age for the origin of the lower Congo River rapids, one of the most extreme freshwater habitats on earth.

The Causes Of Species Richness Patterns Across Space, Time, And Clades And The Role Of “Ecological Limits”

A major goal of research in ecology and evolution is to explain why species richness varies across habitats, regions, and clades. Recent reviews have argued that species richness patterns among regions and clades may be explained by "ecological limits" on diversity over time, which are said to offer an alternative explanation to those invoking speciation and extinction (diversification) and time. Further, it has been proposed that this hypothesis is best supported by failure to find a positive relationship between time (e.g., clade age) and species richness. Here, I critically review the evidence for these claims, and propose how we might better study the ecological and evolutionary origins of species richness patterns. In fact, ecological limits can only influence species richness in clades by influencing speciation and extinction, and so this new "alternative paradigm" is simply one facet of the traditional idea that ecology influences diversification. The only direct evidence for strict ecological limits on richness (i.e., constant diversity over time) is from the fossil record, but many studies cited as supporting this pattern do not, and there is evidence for increasing richness over time. Negative evidence for a relationship between clade age and richness among extant clades is not positive evidence for constant diversity over time, and many recent analyses finding no age-diversity relationship were biased to reach this conclusion. More comprehensive analyses strongly support a positive age-richness relationship. There is abundant evidence that both time and ecological influences on diversification rates are important drivers of both large-scale and small-scale species richness patterns. The major challenge for future studies is to understand the ecological and evolutionary mechanisms underpinning the relationships between time, dispersal, diversification, and species richness patterns.

Improved Integration Time Estimation of Endogenous Retroviruses with Phylogenetic Data

BackgroundEndogenous retroviruses (ERVs) are genetic fossils of ancient retroviral integrations that remain in the genome of many organisms. Most loci are rendered non-functional by mutations, but several intact retroviral genes are known in mammalian genomes. Some have been adopted by the host species, while the beneficial roles of others remain unclear. Besides the obvious possible immunogenic impact from transcribing intact viral genes, endogenous retroviruses have also become an interesting and useful tool to study phylogenetic relationships. The determination of the integration time of these viruses has been based upon the assumption that both 5′ and 3′ Long Terminal Repeats (LTRs) sequences are identical at the time of integration, but evolve separately afterwards. Similar approaches have been using either a constant evolutionary rate or a range of rates for these viral loci, and only single species data. Here we show the advantages of using different approaches.ResultsWe show that there are strong advantages in using multiple species data and state-of-the-art phylogenetic analysis. We incorporate both simple phylogenetic information and Monte Carlo Markov Chain (MCMC) methods to date the integrations of these viruses based on a relaxed molecular clock approach over a Bayesian phylogeny model and applied them to several selected ERV sequences in primates. These methods treat each ERV locus as having a distinct evolutionary rate for each LTR, and make use of consensual speciation time intervals between primates to calibrate the relaxed molecular clocks.ConclusionsThe use of a fixed rate produces results that vary considerably with ERV family and the actual evolutionary rate of the sequence, and should be avoided whenever multi-species phylogenetic data are available. For genome-wide studies, the simple phylogenetic approach constitutes a better alternative, while still being computationally feasible.

Estimating Divergence Time and Ancestral Effective Population Size of Bornean and Sumatran Orangutan Subspecies Using a Coalescent Hidden Markov Model

Due to genetic variation in the ancestor of two populations or two species, the divergence time for DNA sequences from two populations is variable along the genome. Within genomic segments all bases will share the same divergence—because they share a most recent common ancestor—when no recombination event has occurred to split them apart. The size of these segments of constant divergence depends on the recombination rate, but also on the speciation time, the effective population size of the ancestral population, as well as demographic effects and selection. Thus, inference of these parameters may be possible if we can decode the divergence times along a genomic alignment. Here, we present a new hidden Markov model that infers the changing divergence (coalescence) times along the genome alignment using a coalescent framework, in order to estimate the speciation time, the recombination rate, and the ancestral effective population size. The model is efficient enough to allow inference on whole-genome data sets. We first investigate the power and consistency of the model with coalescent simulations and then apply it to the whole-genome sequences of the two orangutan sub-species, Bornean (P. p. pygmaeus) and Sumatran (P. p. abelii) orangutans from the Orangutan Genome Project. We estimate the speciation time between the two sub-species to be thousand years ago and the effective population size of the ancestral orangutan species to be , consistent with recent results based on smaller data sets. We also report a negative correlation between chromosome size and ancestral effective population size, which we interpret as a signature of recombination increasing the efficacy of selection.

Phylogenetic relationships of elephant‐shrews (Afrotheria, Macroscelididae)

Elephant-shrews or sengis (Macroscelidea, Afrotheria) are grouped into two subfamilies, Rhynchocyoninae with a single genus and four species, and Macroscelidinae represented by three genera and 13 species. Our current understanding of the evolutionary relationships within this group is largely based on a molecular phylogeny that suffers from incomplete species representation. We present the first complete phylogeny (with the exception of the recently described East African Rhynchocyon udzungwensis) for Macroscelidea based on mitochondrial and nuclear markers. Novel cytogenetic characters as well as previously described allozyme variation and various morphological features are evaluated and mapped to the molecular topology. Our analyses indicate that Elephantulus is paraphyletic, and that Petrodromus and Macroscelides should be subsumed in Elephantulus. A relaxed Bayesian dating approach supports the hypothesis that an arid-adapted Macroscelidinae lineage dispersed from east Africa at ∼11.5 MYA via an African arid corridor to south-western Africa. The timing of speciation within the east African Rhynchocyoninae (8–10 MYA) is coincidental with the diversification of some other forest specialists. In turn, divergence within the Macroscelidinae coincides with major aridification events across Africa.

Mitochondrial Genomes Reveal Slow Rates of Molecular Evolution and the Timing of Speciation in Beavers (Castor), One of the Largest Rodent Species

BackgroundBeavers are one of the largest and ecologically most distinct rodent species. Little is known about their evolution and even their closest phylogenetic relatives have not yet been identified with certainty. Similarly, little is known about the timing of divergence events within the genus Castor.Methodology/Principal FindingsWe sequenced complete mitochondrial genomes from both extant beaver species and used these sequences to place beavers in the phylogenetic tree of rodents and date their divergence from other rodents as well as the divergence events within the genus Castor. Our analyses support the phylogenetic position of beavers as a sister lineage to the scaly tailed squirrel Anomalurus within the mouse related clade. Molecular dating places the divergence time of the lineages leading to beavers and Anomalurus as early as around 54 million years ago (mya). The living beaver species, Castor canadensis from North America and Castor fiber from Eurasia, although similar in appearance, appear to have diverged from a common ancestor more than seven mya. This result is consistent with the hypothesis that a migration of Castor from Eurasia to North America as early as 7.5 mya could have initiated their speciation. We date the common ancestor of the extant Eurasian beaver relict populations to around 210,000 years ago, much earlier than previously thought. Finally, the substitution rate of Castor mitochondrial DNA is considerably lower than that of other rodents. We found evidence that this is correlated with the longer life span of beavers compared to other rodents.Conclusions/SignificanceA phylogenetic analysis of mitochondrial genome sequences suggests a sister-group relationship between Castor and Anomalurus, and allows molecular dating of species divergence in congruence with paleontological data. The implementation of a relaxed molecular clock enabled us to estimate mitochondrial substitution rates and to evaluate the effect of life history traits on it.

Incomplete lineage sorting patterns among human, chimpanzee, and orangutan suggest recent orangutan speciation and widespread selection

We search the complete orangutan genome for regions where humans are more closely related to orangutans than to chimpanzees due to incomplete lineage sorting (ILS) in the ancestor of human and chimpanzees. The search uses our recently developed coalescent hidden Markov model (HMM) framework. We find ILS present in ∼1% of the genome, and that the ancestral species of human and chimpanzees never experienced a severe population bottleneck. The existence of ILS is validated with simulations, site pattern analysis, and analysis of rare genomic events. The existence of ILS allows us to disentangle the time of isolation of humans and orangutans (the speciation time) from the genetic divergence time, and we find speciation to be as recent as 9-13 million years ago (Mya; contingent on the calibration point). The analyses provide further support for a recent speciation of human and chimpanzee at ∼4 Mya and a diverse ancestor of human and chimpanzee with an effective population size of about 50,000 individuals. Posterior decoding infers ILS for each nucleotide in the genome, and we use this to deduce patterns of selection in the ancestral species. We demonstrate the effect of background selection in the common ancestor of humans and chimpanzees. In agreement with predictions from population genetics, ILS was found to be reduced in exons and gene-dense regions when we control for confounding factors such as GC content and recombination rate. Finally, we find the broad-scale recombination rate to be conserved through the complete ape phylogeny.

Comparative and demographic analysis of orang-utan genomes

“Orangutan” is derived from the Malay term “man of the forest” and aptly describes the Southeast Asian great apes native to Sumatra and Borneo. The orangutan species, Pongo abelii (Sumatran) and Pongo pygmaeus (Bornean), are the most phylogenetically distant great apes from humans, thereby providing an informative perspective on hominid evolution. Here we present a Sumatran orangutan draft genome assembly and short read sequence data from five Sumatran and five Bornean orangutan genomes. Our analyses reveal that, compared to other primates, the orangutan genome has many unique features. Structural evolution of the orangutan genome has proceeded much more slowly than other great apes, evidenced by fewer rearrangements, less segmental duplication, a lower rate of gene family turnover and surprisingly quiescent Alu repeats, which have played a major role in restructuring other primate genomes. We also describe the first primate polymorphic neocentromere, found in both Pongo species, emphasizing the gradual evolution of orangutan genome structure. Orangutans have extremely low energy usage for a eutherian mammal1, far lower than their hominid relatives. Adding their genome to the repertoire of sequenced primates illuminates new signals of positive selection in several pathways including glycolipid metabolism. From the population perspective, both Pongo species are deeply diverse; however, Sumatran individuals possess greater diversity than their Bornean counterparts, and more species-specific variation. Our estimate of Bornean/Sumatran speciation time, 400k years ago (ya), is more recent than most previous studies and underscores the complexity of the orangutan speciation process. Despite a smaller modern census population size, the Sumatran effective population size (Ne) expanded exponentially relative to the ancestral Ne after the split, while Bornean Ne declined over the same period. Overall, the resources and analyses presented here offer new opportunities in evolutionary genomics, insights into hominid biology, and an extensive database of variation for conservation efforts.

Relative effects of time for speciation and tropical niche conservatism on the latitudinal diversity gradient of phyllostomid bats

Determinants of contemporary patterns of diversity, particularly those spanning extensive latitudinal gradients, are some of the most intensely debated issues in ecology. Recently, focus has shifted from a contemporary environmental perspective to a historical one in an attempt to better understand the construction of latitudinal gradients. Although the vast majority of research on historical mechanisms has focused on tropical niche conservatism (TNC), other historical scenarios could produce similar latitudinal gradients. Herein, I formalize predictions to distinguish between two such historical processes--namely time for speciation (TFS) and TNC--and test relative support based on diversity gradients of New World bats. TFS and TNC are distinctly spatial and environmental mechanisms, respectively. Nonetheless, because of the way that environmental characteristics vary spatially, these two mechanisms are hard to distinguish. Evidence provided herein suggests that TNC has had a more important effect than TFS in determining diversity gradients of New World bats. Indeed, relative effects of different historical mechanisms, as well as relative effects of historical and contemporary environmental determinants, are probably context-dependent. Future research should move away from attempting to identify the mechanism with primacy and instead attempt to understand the particular contexts in which different mechanisms have greater influence on diversity gradients.

Studying the Evolution of Promoter Sequences: A Waiting Time Problem

To gain a better understanding of the evolutionary dynamics of regulatory DNA sequences, we address the following questions: (1) How long does it take until a given transcription factor (TF) binding site emerges at random in a promoter sequence? and (2) How does the composition of a TF binding site affect this waiting time? Using two different probabilistic models (an i.i.d. model and a neighbor dependent model), we can compute the expected waiting time for every k-mer, k ranging from 5 to 10, until it appears in a promoter of a species. Our findings indicate that new TF binding sites can be created on a short evolutionary time scale, i.e. in a time span below the speciation time of human and chimp. Furthermore, one can conclude that the composition of a TF binding site plays a crucial role concerning the waiting time until it appears and that the CpG methylation-deamination substitution process probably accelerates the creation of new TF binding sites. A screening of existing TF binding sites moreover reveals that k-mers predicted to have short waiting times occur more frequently than others. Supplementary Material is available at www.libertonline.com/cmb .

Taxonomy of the Oulimnius tuberculatus species group (Coleoptera: Elmidae) based on molecular and morphological data

Two mitochondrial (cytochrome oxidase subunit I, 16S RNA) and one nuclear (18S RNA) gene fragments were used to analyse relationships within the Oulimnius tuberculatus species group. The results of molecular data analysis are compared with morphological characters, and the distributional patterns and taxonomic status of recognized taxa are addressed. Based on molecular data, Oulimnius perezi is re-validated as a distinct species, and the discovery of a possible new species from northwest Italy is reported. The possible origins and times of speciation within the species group are discussed.

High-temperature Mossbauer spectroscopy: A probe for the relaxation time of Fe species in silicate melts and glasses

The Mössbauer spectra of an albite glass and melt doped with 57Fe (bulk composition NaFe0.04AlSi3O8) were measured in situ to 1100 °C. A specially designed furnace was used where a disk of the sample was enclosed in a capsule of graphite. The furnace was purged with argon to avoid oxidation of the graphite, and shields of boron nitride (BN) were used to protect both the γ-ray source and the detector from thermal radiation. Room-temperature spectra show contributions from paramagnetic Fe2+, paramagnetic Fe3+, and magnetic Fe3+. The signal of Fe2+ disappears around 400 °C, and the signal of Fe3+ disappears at about 1100 °C. This behavior cannot be due to changes in the oxidation state of iron because in situ visible and near infrared spectra of the same sample show that Fe2+ persists to at least 1000 °C and the quenched samples do not show any change in oxidation state. Rather, the disappearance of Fe2+ and Fe3+ in the spectra is likely due to the structural relaxation time around these cations becoming comparable to the Mössbauer timescale (lifetime of excited state ≈ 10-8 s). We show that the temperature at which the Fe3+ contribution disappears corresponds to the expected glass transition temperature of a “ferrialbite” NaFeSi3O8 melt for a timescale of 10-8 s. Our data therefore confirm that viscous flow is due to the rearrangement of the chemical bonds between oxygen anions and network-forming cations. Furthermore, our data show that Mössbauer spectroscopy can be used to study the speciation and relaxation time around iron in silicate melts even at temperatures above the macroscopic glass transition temperature as defined from viscosimetry and calorimetry.

Multiple hybridization events between Drosophila simulans and Drosophila mauritiana are supported by mtDNA introgression.

The study of speciation has advanced considerably in the last decades because of the increased application of molecular tools. In particular, the quantification of gene flow between recently diverged species could be addressed. Drosophila simulans and Drosophila mauritiana diverged, probably allopatrically, from a common ancestor approximately 250 000 years ago. However, these species share one mitochondrial DNA (mtDNA) haplotype indicative of a recent episode of introgression. To study the extent of gene flow between these species, we took advantage of a large sample of D. mauritiana and employed a range of different markers, i.e. nuclear and mitochondrial sequences, and microsatellites. This allowed us to detect two new mtDNA haplotypes (MAU3 and MAU4). These haplotypes diverged quite recently from haplotypes of the siII group present in cosmopolitan populations of D. simulans. The mean divergence time of the most diverged haplotype (MAU4) is approximately 127 000 years, which is more than 100 000 years before the assumed speciation time. Interestingly, we also found some evidence for gene flow at the nuclear level because an excess of putatively neutral loci shows significantly reduced differentiation between D. simulans and D. mauritiana. Our results suggest that these species are exchanging genes more frequently than previously thought.

Evolutionary history of the four-spotted megrim ( Lepidorhombus boscii) and speciation time within the genus based on mitochondrial genes analysis

The evolutionary history and geographic distribution of North-Atlantic and Mediterranean marine taxa has been largely affected by past geological and climatic events, like the Messinian salinity crisis, the opening of the Strait of Gibraltar and the Quaternary glacial cycles. The four-spotted megrim Lepidorhombus boscii is a demersal flatfish of the family Scophthalmidae (Pleuronectiformes), distributed in the Northeast Atlantic and the Mediterranean Sea. During its larval development it is planktonic, being passively drifted by marine currents, while adults are more or less sedentary living near the sea bottom. In order to investigate whether past geological and climatic events have influenced the evolutionary and demographic history of L. boscii, we analyzed a fragment of the highly variable mitochondrial control region in 163 individuals from different North-Atlantic areas and from the Mediterranean Sea. Contemporary processes of moderate gene flow, partially restricted by isolation by distance, as well as recent paleoecological events like the last Pleistocene glaciation, seem to play key roles in shaping the current phylogeographic pattern of the four-spotted megrim. On the other hand, we also analyzed 94 individuals from different North-Atlantic areas of its congeneric species L. whiffiagonis in order to compare genetic variation patterns within this genus. Finally, we used a fragment of the protein-coding mitochondrial gene cytochrome c oxidase I to estimate the time of speciation in megrims. Results suggest that divergence between the two species likely took place 5.3 MYA, which can be correlated with the end of the Messinian salinity crisis.

Speciation and phylogeography of giant petrels Macronectes

We examine global phylogeography of the two forms of giant petrel Macronectes spp. Although previously considered to be a single taxon, and despite debate over the status of some populations and the existence of minimal genetic data (one mitochondrial cytochrome b sequence per form), the current consensus based on morphology is that there are two species, Northern Giant Petrel M. halli and Southern Giant Petrel M. giganteus. This study examined genetic variation at cytochrome b as well as six microsatellite loci in giant petrels from 22 islands, representing most island groups at which the two species breed. Both markers support separate species status, although sequence divergence in cytochrome b was only 0.42% (corrected). Divergence was estimated to have occurred approximately 0.2mya, but with some colonies apparently separated for longer (up to 0.5 my). Three clades were found within giant petrels, which separated approximately 0.7mya, with the Southern Giant Petrel paraphyletic to a monophyletic Northern Giant Petrel. There was evidence of past fragmentation during the Pleistocene, with subsequent secondary contact within Southern Giant Petrels. The analysis also suggested a period of past population expansion that corresponded roughly to the timing of speciation and the separation of an ancestral giant petrel population from the fulmar Fulmarus clade.

Highly improved dating of primate ERV integrations

Endogenous retroviruses (ERVs) are genetic fossils of ancient retroviral integrations that remain in the genome of many organisms. Because these remnants are present in many related species, they have become an interesting and useful tool to study phylogenetic relationships [1]. The determination of the insertion time of these viruses has been based upon the assumption that both 5' and 3' Long Terminal Repeats (LTRs) sequences are identical at the time of insertion, but evolve separately afterwards. Similar approaches have been using either a constant evolutionary rate or a range of rates for these viral loci, and only single species data. These methods, however, are based on a very general and wrong assumption: that both LTRs evolve at the same rate [2] (figure ​(figure1).1). Instead, we show that there are strong advantages in using multiple species data and state-of-the-art phylogenetic analysis. We incorporate both simple phylogenetic information and Monte Carlo Markov Chain (MCMC) methods to date the insertions of these viruses based on a relaxed molecular clock approach over a Bayesian phylogeny model and applied them to several selected ERV sequences in primates. These methods treat each ERV locus as having two distinct evolutionary rates for each LTR, and make use of consensual speciation time intervals between primates to calibrate the relaxed molecular clocks (figure ​(figure2).2). Our results show strong improvements when applying simple inference methods that take in account the obtained branch lengths and is computationally inexpensive. Figure 1 Variation between 3' and 5' LTR rates in studied loci as opposed to an uniform rate. Figure 2 Estimation of insertion times based on multi-species phylogenetic data. Known speciation times (T1) can be used in a relaxed molecular clock approach in order to assess the estimated insertion time (T2).

Speciation as an active force in promoting genetic evolution

There is a growing appreciation among evolutionary biologists that the rate and tempo of molecular evolution might often be altered at or near the time of speciation, i.e. that speciation is in some way a special time for genes. Molecular phylogenies frequently reveal increased rates of genetic evolution associated with speciation and other lines of investigation suggest that various types of abrupt genomic disruption can play an important role in promoting speciation via reproductive isolation. These phenomena are in conflict with the gradual view of molecular evolution that is implicit in much of our thinking about speciation and in the tools of modern biology. This raises the prospect of studying the molecular evolutionary consequences of speciation per se and studying the footprint of speciation as an active force in promoting genetic divergence. Here we discuss the reasons to believe that speciation can play such a role and elaborate on possible mechanisms for accelerated rates of evolution following speciation. We provide an example of how it is possible detect whether accelerated bursts of evolution occur in neutral and/or adaptive regions of genes and discuss the implications of rapid episodes of change for conventional models of molecular evolution. Speciation might often owe more to ephemeral and essentially arbitrary events that cause reproductive isolation than to the gradual and regular tug of natural selection that draws a species into a new niche.

Can the tropical conservatism hypothesis explain temperate species richness patterns? An inverse latitudinal biodiversity gradient in the New World snake tribe Lampropeltini

ABSTRACTAim A latitudinal gradient in species richness, defined as a decrease in biodiversity away from the equator, is one of the oldest known patterns in ecology and evolutionary biology. However, there are also many known cases of increasing poleward diversity, forming inverse latitudinal biodiversity gradients. As only three processes (speciation, extinction and dispersal) can directly affect species richness in areas, similar factors may be responsible for both classical (high tropical diversity) and inverse (high temperate diversity) gradients. Thus, a modified explanation for differential species richness which accounts for both patterns would be preferable to one which only explains high tropical biodiversity.Location The New World.Methods We test several proposed ecological, temporal, evolutionary and spatial explanations for latitudinal diversity gradients in the New World snake tribe Lampropeltini, which exhibits its highest biodiversity in temperate regions.Results We find that an extratropical peak in species richness is not explained by latitudinal variation in diversification rate, the mid‐domain effect, or Rapoport's rule. Rather, earlier colonization and longer duration in the temperate zones allowing more time for speciation to increase biodiversity, phylogenetic niche conservatism limiting tropical dispersal and the expansion of the temperate zones in the Tertiary better explain inverse diversity gradients in this group.Main conclusions Our conclusions are the inverse of the predictions made by the tropical conservatism hypothesis to explain higher biodiversity near the equator. Therefore, we suggest that the processes invoked are not intrinsic to the tropics but are dependent on historical biogeography to determine the distribution of species richness, which we refer to as the ‘biogeographical conservatism hypothesis’.

Maximum tree: a consistent estimator of the species tree

We propose a model based approach to use multiple gene trees to estimate the species tree. The coalescent process requires that gene divergences occur earlier than species divergences when there is any polymorphism in the ancestral species. Under this scenario, speciation times are restricted to be smaller than the corresponding gene split times. The maximum tree (MT) is the tree with the largest possible speciation times in the space of species trees restricted by available gene trees. If all populations have the same population size, the MT is the maximum likelihood estimate of the species tree. It can be shown the MT is a consistent estimator of the species tree even when the MT is built upon the estimates of the true gene trees if the gene tree estimates are statistically consistent. The MT converges in probability to the true species tree at an exponential rate.