Abstract:
:Mouse lemurs (Microcebus) are a radiation of morphologically cryptic primates distributed throughout Madagascar for which the number of recognized species has exploded in the past two decades. This taxonomic revision has prompted understandable concern that there has been substantial oversplitting in the mouse lemur clade. Here, we investigate mouse lemur diversity in a region in northeastern Madagascar with high levels of microendemism and predicted habitat loss. We analyzed RADseq data with multispecies coalescent (MSC) species delimitation methods for two pairs of sister lineages that include three named species and an undescribed lineage previously identified to have divergent mtDNA. Marked differences in effective population sizes, levels of gene flow, patterns of isolation-by-distance, and species delimitation results were found among the two pairs of lineages. Whereas all tests support the recognition of the presently undescribed lineage as a separate species, the species-level distinction of two previously described species, M. mittermeieri and M. lehilahytsara is not supported - a result that is particularly striking when using the genealogical discordance index (gdi). Non-sister lineages occur sympatrically in two of the localities sampled for this study, despite an estimated divergence time of less than 1 Ma. This suggests rapid evolution of reproductive isolation in the focal lineages, and in the mouse lemur clade generally. The divergence time estimates reported here are based on the MSC calibrated with pedigree-based mutation rates and are considerably more recent than previously published fossil-calibrated relaxed-clock estimates. We discuss the possible explanations for this discrepancy, noting that there are theoretical justifications for preferring the MSC estimates in this case.
journal_name
Syst Bioljournal_title
Systematic biologyauthors
Poelstra J,Salmona J,Tiley GP,Schüßler D,Blanco MB,Andriambeloson JB,Bouchez O,Campbell CR,Etter PD,Hohenlohe PA,Hunnicutt KE,Iribar A,Johnson EA,Kappeler PM,Larsen PA,Manzi S,Ralison JM,Randrianambinina B,Rasoloarisodoi
10.1093/sysbio/syaa053subject
Has Abstractpub_date
2020-07-08 00:00:00eissn
1063-5157issn
1076-836Xpii
5869053pub_type
杂志文章abstract::All current phylogenetic methods assume that DNA substitutions are independent among sites. However, ample empirical evidence suggests that the process of substitution is not independent but is, in fact, temporally and spatially correlated. The robustness of several commonly used phylogenetic methods to the assumption...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1080/106351599260319
更新日期:1999-06-01 00:00:00
abstract::Polyploidization is an important speciation mechanism in the barley genus Hordeum. To analyze evolutionary changes after allopolyploidization, knowledge of parental relationships is essential. One chloroplast and 12 nuclear single-copy loci were amplified by polymerase chain reaction (PCR) in all Hordeum plus six out-...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1093/sysbio/syv035
更新日期:2015-09-01 00:00:00
abstract::Several methods have been proposed to infer the states at the ancestral nodes on a phylogeny. These methods assume a specific tree and set of branch lengths when estimating the ancestral character state. Inferences of the ancestral states, then, are conditioned on the tree and branch lengths being true. We develop a h...
journal_title:Systematic biology
pub_type: 杂志文章
doi:
更新日期:2001-06-01 00:00:00
abstract::This article reviews the various models that have been used to describe the relationships between gene trees and species trees. Molecular phylogeny has focused mainly on improving models for the reconstruction of gene trees based on sequence alignments. Yet, most phylogeneticists seek to reveal the history of species....
journal_title:Systematic biology
pub_type: 杂志文章,评审
doi:10.1093/sysbio/syu048
更新日期:2015-01-01 00:00:00
abstract::Two lines of evidence indicate that the degree of symmetry in phylogenetic topologies differs at different hierarchical levels. First, in a set of 61 phylogenies with superspecific taxa as their terminals, trees were on average more unbalanced (asymmetric) when the species richness of terminals was considered than whe...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1080/10635150290102546
更新日期:2002-12-01 00:00:00
abstract::We collected ~29 kb of sequence data using Roche 454 pyrosequencing in order to estimate the timing and pattern of diversification in the carnivorous pitcher plant Sarracenia alata. Utilizing modified protocols for reduced representation library construction, we generated sequence data from 86 individuals across 10 po...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1093/sysbio/sys048
更新日期:2012-10-01 00:00:00
abstract::Sampling across tree space is one of the major challenges in Bayesian phylogenetic inference using Markov chain Monte Carlo (MCMC) algorithms. Standard MCMC tree moves consider small random perturbations of the topology, and select from candidate trees at random or based on the distance between the old and new topolog...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1093/sysbio/syaa002
更新日期:2020-09-01 00:00:00
abstract::The Noah's Ark Problem (NAP) is a comprehensive cost-effectiveness methodology for biodiversity conservation that was introduced by Weitzman (1998) and utilizes the phylogenetic tree containing the taxa of interest to assess biodiversity. Given a set of taxa, each of which has a particular survival probability that ca...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1080/10635150600873876
更新日期:2006-08-01 00:00:00
abstract::Markov chain Monte Carlo (MCMC) is a methodology that is gaining widespread use in the phylogenetics community and is central to phylogenetic software packages such as MrBayes. An important issue for users of MCMC methods is how to select appropriate values for adjustable parameters such as the length of the Markov ch...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1080/10635150600812544
更新日期:2006-08-01 00:00:00
abstract::Phylogenomic and paleontological data constitute complementary resources for unravelling the phylogenetic relationships and divergence times of lineages, yet few studies have attempted to fully integrate them. Several unique properties of echinoids (sea urchins) make them especially useful for such synthetizing approa...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1093/sysbio/syaa069
更新日期:2020-09-03 00:00:00
abstract::The obligate mutualism between pollinating fig wasps in the family Agaonidae (Hymenoptera: Chalcidoidea) and Ficus species (Moraceae) is often regarded as an example of co-evolution but little is known about the history of the interaction, and understanding the origin of functionally dioecious fig pollination has been...
journal_title:Systematic biology
pub_type: 杂志文章
doi:
更新日期:2001-04-01 00:00:00
abstract::Population structure influences genealogical patterns, however, data pertaining to how populations are structured are often unavailable or not directly observable. Inference of population structure is highly important in molecular epidemiology where pathogen phylogenetics is increasingly used to infer transmission pat...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1093/sysbio/syaa009
更新日期:2020-09-01 00:00:00
abstract::Genome-scale data offer the opportunity to clarify phylogenetic relationships that are difficult to resolve with few loci, but they can also identify genomic regions with evolutionary history distinct from that of the species history. We collected whole-genome sequence data from 29 taxa in the legume genus Medicago, t...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1093/sysbio/syt009
更新日期:2013-05-01 00:00:00
abstract::The congruence between the order of cladistic branching and the first appearance dates of fossil lineages can be quantified using a variety of indices. Good matching is a prerequisite for the accurate time calibration of trees, while the distribution of congruence indices across large samples of cladograms has underpi...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1093/sysbio/syw039
更新日期:2016-09-01 00:00:00
abstract::Hybridization is an important evolutionary mechanism in plants and has been increasingly documented in animals. Difficulty in reconstruction of reticulate evolution, however, has been a long-standing problem in phylogenetics. Consequently, hybrid speciation may play a major role in causing topological incongruence bet...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1080/10635159950127321
更新日期:2000-09-01 00:00:00
abstract::Gene trees record the combination of gene-level events, such as duplication, transfer and loss (DTL), and species-level events, such as speciation and extinction. Gene tree-species tree reconciliation methods model these processes by drawing gene trees into the species tree using a series of gene and species-level eve...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1093/sysbio/syt054
更新日期:2013-11-01 00:00:00
abstract::We develop a Bayesian method for inferring the species phylogeny under the multispecies coalescent (MSC) model. To improve the mixing properties of the Markov chain Monte Carlo (MCMC) algorithm that traverses the space of species trees, we implement two efficient MCMC proposals: the first is based on the Subtree Pruni...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1093/sysbio/syw119
更新日期:2017-09-01 00:00:00
abstract::When doing a bootstrap analysis with a single tree saved per pseudoreplicate, biased search algorithms may influence support values more than actual properties of the data set. Two methods commonly used for finding phylogenetic trees consist of randomizing the input order of species in multiple addition sequences foll...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1093/sysbio/syu051
更新日期:2014-11-01 00:00:00
abstract::Historically, comparisons of host and parasite phylogenies have concentrated on cospeciation. However, many of these comparisons have demonstrated that the phylogenies of hosts and parasites are seldom completely congruent, suggesting that phenomena other than cospeciation play an important role in the evolution of ho...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1080/10635150490265085
更新日期:2004-02-01 00:00:00
abstract::The phylogenetic comparative method uses estimates of evolutionary relationships to explicitly model the covariance structure of interspecific data. By accounting for common ancestry, the coevolution between 2 or more traits, as a response to one another or to environmental variables, can be studied without confoundin...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1093/sysbio/syq098
更新日期:2011-05-01 00:00:00
abstract::In the Bayesian paradigm, a common method for comparing two models is to compute the Bayes factor, defined as the ratio of their respective marginal likelihoods. In recent phylogenetic works, the numerical evaluation of marginal likelihoods has often been performed using the harmonic mean estimation procedure. In the ...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1080/10635150500433722
更新日期:2006-04-01 00:00:00
abstract::Acoela are marine microscopic worms currently thought to be the sister taxon of all other bilaterians. Acoels have long been used as models in evolutionary scenarios, and generalized conclusions about acoel and bilaterian ancestral features are frequently drawn from studies of single acoel species. There is no extensi...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1093/sysbio/syr073
更新日期:2011-12-01 00:00:00
abstract::Correct rooting of the angiosperm radiation is both challenging and necessary for understanding the origins and evolution of physiological and phenotypic traits in flowering plants. The problem is known to be difficult due to the large genetic distance separating flowering plants from other seed plants and the sparse ...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1093/sysbio/sys070
更新日期:2013-01-01 00:00:00
abstract::There has long been ambiguity in the use of the term tree in phylogenetic systematics, which is a continuous source of misinterpretation of evolutionary relationships. The basic problem is that while many trees with phylogenetic or evolutionary relevance, such as cladograms, are consistent with graph theory, tree-like...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1093/sysbio/syx039
更新日期:2017-09-01 00:00:00
abstract::Platyrrhine primates and caviomorph rodents are clades of mammals that colonized South America during its period of isolation from the other continents, between 100 and 3 million years ago (Mya). Until now, no molecular study investigated the timing of the South American colonization by these two lineages with the sam...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1080/10635150500481390
更新日期:2006-04-01 00:00:00
abstract::Characters derived from advertisement calls, morphology, allozymes, and the sequences of the small subunit of the mitochondrial ribosomal gene (12S) and the cytochrome oxidase I (COI) mitochondrial gene were used to estimate the phylogeny of frogs of the Physalaemus pustulosus group (Leptodactylidae). The combinabilit...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1080/106351598260932
更新日期:1998-06-01 00:00:00
abstract::Young polyploid events are easily diagnosed by various methods, but older polyploid events become increasingly difficult to identify as chromosomal rearrangements, tandem gene or partial chromosome duplications, changes in substitution rates among duplicated genes, pseudogenization or locus loss, and interlocus intera...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1080/10635150590945359
更新日期:2005-06-01 00:00:00
abstract::The Amazon and neighboring South American river basins harbor the world's most diverse assemblages of freshwater fishes. One of the most prominent South American fish families is the Serrasalmidae (pacus and piranhas), found in nearly every continental basin. Serrasalmids are keystone ecological taxa, being some of th...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1093/sysbio/syaa065
更新日期:2020-08-12 00:00:00
abstract::Targeted sequence capture is becoming a widespread tool for generating large phylogenomic data sets to address difficult phylogenetic problems. However, this methodology often generates data sets in which increasing the number of taxa and loci increases amounts of missing data. Thus, a fundamental (but still unresolve...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1093/sysbio/syv058
更新日期:2016-01-01 00:00:00
abstract::The insect order Psocodea is a diverse lineage comprising both parasitic (Phthiraptera) and non-parasitic members (Psocoptera). The extreme age and ecological diversity of the group may be associated with major genomic changes, such as base compositional biases expected to affect phylogenetic inference. Divergent morp...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1093/sysbio/syaa075
更新日期:2020-09-26 00:00:00