Systematic Biology (SYST BIOL)
Systematic Biology is the bimonthly journal of the Society of Systematic Biologists. Papers for the journal are original contributions to the theory, principles, and methods of systematics as well as phylogeny, evolution, morphology, biogeography, paleontology, genetics, and the classification of all living things. A Points of View section offers a forum for discussion, while book reviews and announcements of general interest are also featured.
- Impact factor10.23Show impact factor historyHide impact factor history
- WebsiteSystematic Biology website
Other titlesSystematic biology (Online), Systematic biology
Material typeDocument, Periodical, Internet resource
Document typeInternet Resource, Computer File, Journal / Magazine / Newspaper
- Author can archive a pre-print version
- Author cannot archive a post-print version
- 12 month embargo for STM, Behavioural Science and Public Health Journals
- 18 month embargo for SSH journals
- Some individual journals may have policies prohibiting pre-print archiving
- Pre-print on authors own website, Institutional or Subject Repository
- Post-print on authors own website, Institutional or Subject Repository
- Publisher's version/PDF cannot be used
- On a non-profit server
- Published source must be acknowledged
- Must link to publisher version
- Set statements to accompany deposits (see policy)
- Publisher will deposit to PMC on behalf of NIH authors.
- STM: Science, Technology and Medicine
- SSH: Social Science and Humanities
- 'Taylor & Francis (Psychology Press)' is an imprint of 'Taylor & Francis'
Publications in this journal
Article: Book Review: Systematics and Biogeography: Cladistics and Vicariance.—Gareth Nelson and Norman I. Platnick. Columbia University Press, 1981. xi+567 pp. ISBN 0- 231-04574-3 (hardback).Systematic Biology 01/2010; 59(5):612-614.
Article: A review of "The New Taxonomy".Systematic Biology 09/2008; 57(4):660-3.
Systematic Biology 09/2008; 57(4):658-60.
Article: Codivergence in heteromyid rodents (Rodentia: heteromyidae) and their sucking lice of the genus Fahrenholzia (Phthiraptera: anoplura).[show abstract] [hide abstract]
ABSTRACT: Although most studies of codivergence rely primarily on topological comparisons of host and parasite phylogenies, temporal assessments are necessary to determine if divergence events in host and parasite trees occurred contemporaneously. A combination of cophylogenetic analyses and comparisons of branch lengths are used in this study to understand the host-parasite association between heteromyid rodents (Rodentia: Heteromyidae) and their sucking lice of the genus Fahrenholzia (Phthiraptera: Anoplura). Cophylogenetic comparisons based on nucleotide substitutions in the mitochondrial COI gene reveal a significant, but not perfect, pattern of cophylogeny between heteromyids and their sucking lice. Regression analyses show a significant functional relationship between the lengths of analogous branches in the host and parasite trees, indicating that divergence events in hosts and parasites were approximately contemporaneous. Thus, the topological similarity observed between heteromyids and their lice is the result of codivergence. These analyses also show that the COI gene in lice is evolving two to three times faster than the same gene in their hosts (similar to the results of studies of other lice and their vertebrate hosts) and that divergence events in lice occurred shortly after host divergence. We recommend that future studies of codivergence include temporal comparisons and, when possible, use the same molecular marker(s) in hosts and parasites to achieve the greatest insight into the history of the host-parasite relationship.Systematic Biology 07/2008; 57(3):449-65.
[show abstract] [hide abstract]
ABSTRACT: The phylogenetic history of Medicago was examined for 60 accessions from 56 species using two nuclear genes (CNGC5 and beta-cop) and one mitochondrial region (rpS14-cob). The results of several analyses revealed that extensive robustly supported incongruence exists among the nuclear genes, the cause of which we seek to explain. After rejecting several processes, hybridization and lineage sorting of ancestral polymorphisms remained as the most likely factors promoting incongruence. Using coalescence simulations, we rejected lineage sorting alone as an explanation of the differences among gene trees. The results indicate that hybridization has been common and ongoing among lineages since the origin of Medicago. Coalescence provides a good framework to test the causes of incongruence commonly seen among gene trees but requires knowledge of effective population sizes and generation times. We estimated the effective population size at 240,000 individuals and assumed a generation time of 1 year in Medicago (many are annual plants). A sensitivity analysis showed that our conclusions remain unchanged using a larger effective population size and/or longer generation time.Systematic Biology 07/2008; 57(3):466-82.
Systematic Biology 07/2008; 57(3):503-7.
[show abstract] [hide abstract]
ABSTRACT: A new approach for biogeography to find patterns of sympatry, based on network analysis, is proposed. Biogeographic analysis focuses basically on sympatry patterns of species. Sympatry is a network (= relational) datum, but it has never been analyzed before using relational tools such as Network Analysis. Our approach to biogeographic analysis consists of two parts: first the sympatry inference and second the network analysis method (NAM). The sympatry inference method was designed to propose sympatry hypothesis, constructing a basal sympatry network based on punctual data, independent of a priori distributional area determination. In this way, two or more species are considered sympatric when there is interpenetration and relative proximity among their records of occurrence. In nature, groups of species presenting within-group sympatry and between-group allopatry constitute natural units (units of co-occurrence). These allopatric units are usually connected by intermediary species. The network analysis method (NAM) that we propose here is based on the identification and removal of intermediary species to segregate units of co-occurrence, using the betweenness measure and the clustering coefficient. The species ranges of the units of co-occurrence obtained are transferred to a map, being considered as candidates to areas of endemism. The new approach was implemented on three different real complex data sets (one of them a classic example previously used in biogeography) resulting in (1) independence of predefined spatial units; (2) definition of co-occurrence patterns from the sympatry network structure, not from species range similarities; (3) higher stability in results despite scale changes; (4) identification of candidates to areas of endemism supported by strictly endemic species; (5) identification of intermediary species with particular biological attributes.Systematic Biology 07/2008; 57(3):432-48.
Article: A novel test for host-symbiont codivergence indicates ancient origin of fungal endophytes in grasses.[show abstract] [hide abstract]
ABSTRACT: Significant phylogenetic codivergence between plant or animal hosts (H) and their symbionts or parasites (P) indicates the importance of their interactions on evolutionary time scales. However, valid and realistic methods to test for codivergence are not fully developed. One of the systems where possible codivergence has been of interest involves the large subfamily of temperate grasses (Pooideae) and their endophytic fungi (epichloae). These widespread symbioses often help protect host plants from herbivory and stresses and affect species diversity and food web structures. Here we introduce the MRCALink (most-recent-common-ancestor link) method and use it to investigate the possibility of grass-epichloë codivergence. MRCALink applied to ultrametric H and P trees identifies all corresponding nodes for pairwise comparisons of MRCA ages. The result is compared to the space of random H and P tree pairs estimated by a Monte Carlo method. Compared to tree reconciliation, the method is less dependent on tree topologies (which often can be misleading), and it crucially improves on phylogeny-independent methods such as ParaFit or the Mantel test by eliminating an extreme (but previously unrecognized) distortion of node-pair sampling. Analysis of 26 grass species-epichloë species symbioses did not reject random association of H and P MRCA ages. However, when five obvious host jumps were removed, the analysis significantly rejected random association and supported grass-endophyte codivergence. Interestingly, early cladogenesis events in the Pooideae corresponded to early cladogenesis events in epichloae, suggesting concomitant origins of this grass subfamily and its remarkable group of symbionts. We also applied our method to the well-known gopher-louse data set.Systematic Biology 07/2008; 57(3):483-98.
Article: Synonymous substitutions substantially improve evolutionary inference from highly diverged proteins.[show abstract] [hide abstract]
ABSTRACT: Codon-and amino acid-substitution models are widely used for the evolutionary analysis of protein-coding DNA sequences. Using codon models, the amounts of both nonsynonymous and synonymous DNA substitutions can be estimated. The ratio of these amounts represents the strength of selective pressure. Using amino acid models, the amount of nonsynonymous substitutions is estimated, but that of synonymous substitutions is ignored. Although amino acid models lose any information regarding synonymous substitutions, they explicitly incorporate the information for amino acid replacement, which is empirically derived from databases. It is often presumed that when the protein-coding sequences are highly divergent, synonymous substitutions might be saturated and the evolutionary analysis may be hampered by synonymous noise. However, there exists no quantitative procedure to verify whether synonymous substitutions can be ignored; therefore, amino acid models have been arbitrarily selected. In this study, we investigate the issue of a statistical comparison between codon-and amino acid-substitution models. For this purpose, we propose a new procedure to transform a 20-dimensional amino acid model to a 61-dimensional codon model. This transformation reveals that amino acid models belong to a subset of the codon models and enables us to test whether synonymous substitutions can be ignored by using the likelihood ratio. Our theoretical results and analyses of real data indicate that synonymous substitutions are very informative and substantially improve evolutionary inference, even when the sequences are highly divergent. Therefore, we note that amino acid models should be adopted only after carefully investigating and discarding the possibility that synonymous substitutions can reveal important evolutionary information.Systematic Biology 07/2008; 57(3):367-77.
Article: A Review of: "Speciation in Birds"Systematic Biology 07/2008; 57(3):515-516.
Systematic Biology 07/2008; 57(3):499-503.
Article: Estimating evolution of temporal sequence changes: a practical approach to inferring ancestral developmental sequences and sequence heterochrony.[show abstract] [hide abstract]
ABSTRACT: Developmental biology often yields data in a temporal context. Temporal data in phylogenetic systematics has important uses in the field of evolutionary developmental biology and, in general, comparative biology. The evolution of temporal sequences, specifically developmental sequences, has proven difficult to examine due to the highly variable temporal progression of development. Issues concerning the analysis of temporal sequences and problems with current methods of analysis are discussed. We present here an algorithm to infer ancestral temporal sequences, quantify sequence heterochronies, and estimate pseudoreplicate consensus support for sequence changes using Parsimov-based genetic inference [PGi]. Real temporal developmental sequence data sets are used to compare PGi with currently used approaches, and PGi is shown to be the most efficient, accurate, and practical method to examine biological data and infer ancestral states on a phylogeny. The method is also expandable to address further issues in developmental evolution, namely modularity.Systematic Biology 07/2008; 57(3):378-87.
[show abstract] [hide abstract]
ABSTRACT: DNA barcoding as a method for species identification is rapidly increasing in popularity. However, there are still relatively few rigorous methodological tests of DNA barcoding. Current distance-based methods are frequently criticized for treating the nearest neighbor as the closest relative via a raw similarity score, lacking an objective set of criteria to delineate taxa, or for being incongruent with classical character-based taxonomy. Here, we propose an artificial intelligence-based approach - inferring species membership via DNA barcoding with back-propagation neural networks (named BP-based species identification) - as a new advance to the spectrum of available methods. We demonstrate the value of this approach with simulated data sets representing different levels of sequence variation under coalescent simulations with various evolutionary models, as well as with two empirical data sets of COI sequences from East Asian ground beetles (Carabidae) and Costa Rican skipper butterflies. With a 630-to 690-bp fragment of the COI gene, we identified 97.50% of 80 unknown sequences of ground beetles, 95.63%, 96.10%, and 100% of 275, 205, and 9 unknown sequences of the neotropical skipper butterfly to their correct species, respectively. Our simulation studies indicate that the success rates of species identification depend on the divergence of sequences, the length of sequences, and the number of reference sequences. Particularly in cases involving incomplete lineage sorting, this new BP-based method appears to be superior to commonly used methods for DNA-based species identification.Systematic Biology 05/2008; 57(2):202-15.
Data provided are for informational purposes only. Although carefully collected, accuracy cannot be guaranteed. The impact factor represents a rough estimation of the journal's impact factor and does not reflect the actual current impact factor. Publisher conditions are provided by RoMEO. Differing provisions from the publisher's actual policy or licence agreement may be applicable.
ISSN: 1879-0534, Impact factor: 1.27
ISSN: 1879-0429, Impact factor: 7.82
ISSN: 1873-5568, Impact factor: 1.56
Applied radiation and isotopes: including data, instrumentation and methods for use in agriculture,...
ISSN: 1872-9800, Impact factor: 1.09
Nature Publishing Group, Nature...
ISSN: 1755-4349, Impact factor: 20.52
Deutsche Zoologische Gesellschaft
ISSN: 1742-9994, Impact factor: 4.46
Oxford University Press
ISSN: 1742-3406, Impact factor: 0.82