What is a fish species?

The formal processes of alpha-taxonomy ensure that species have uniquenames and can be identified. No similar process is mandatory forinfraspecific variation, so the species is a uniquely importantpractical term. At present, there is little agreement of the definitionof a species. In the last 30 years, numerous concepts have beenproposed. The nature of fish species is reviewed. Clonal inheritance ofnuclear genes occurs in several lineages. Hybridization is frequent,often leading to introgression, which may lead to extinction of species.Species may have hybrid origins. There is good evidence for parallelspeciation in similar habitats. There are clearly exceptions to thecladistic assumption of dichotomous branching during speciation. Siblingspecies may exist with no discernible niche differentiation.Basic assumptions are violated for the recognition, phylogenetic,ecological and some formulations of the evolutionary species concepts.The most satisfactory definitions are two of the earliest proposed inthe light of evolutionary theory. The Darwinian view is that species arerecognizable entities which are not qualitatively distinct fromvarieties. A restatement of this concept in genetic terms provides ameans of dealing with all forms of species known in present-day fishes.This modified Darwinian concept is operated through the application offuzzy logic rather than rigid definition. This involves a search fordiscontinuities between species, rather than an a priori definition ofhow boundaries are to be determined. A subset of Darwinian species areMayrian or biological species, which are characterized by theirdemonstrable reproductive isolation from other species. The status of apopulation as a Mayrian species is a testable hypothesis. Moleculartechniques allow this hypothesis to be tested more easily thanpreviously, at least when dealing with sympatric populations.     

A vectorized method of importance sampling with applications to models of mutation and migration

An importance-sampling method is presented for computing the likelihood of the configuration of population genetic data under general assumptions about population history and transitions among states. The configuration of the data is the number of chromosomes sampled that are in each of a finite set of states. Transitions among states are governed by a Markov chain with transition probabilities dependent on one or more parameters. The method assumes that the joint distribution of coalescence times of the underlying gene genealogy is independent of the genetic state of each lineage. Given a set of coalescence times, the probability that a pair of lineages is chosen to coalesce in each replicate is proportional to the contribution that the coalescence event makes to the probability of the data. This method can be applied to gene genealogies generated by the neutral coalescent process and to genealogies generated by other processes, such as a linear birth-death process which provides a good approximation to the dynamics of low-frequency alleles. Two applications are described. In the first, the fit of allele frequencies at two microsatellite loci sampled in a Sardinian population to the one-step mutation model is tested. The one-step model is rejected for one locus but not for the other. The second application is to low-frequency alleles in a geographically subdivided population. The geographic location is the allelic state, and the alleles are assumed to be sufficiently rare that their dynamics can be approximated by a linear birth-death process in which the birth and death rates are independent of geographic location. The analysis of eight low-frequency allozyme alleles found in the glaucous-winged gull, Larus glaucescens, illustrates how geographically restricted dispersal can be detected.     

Historical male‐mediated introgression in horseshoe bats revealed by multilocus DNA sequence data

Instances of hybridization between mammalian taxa in the wild are rarely documented. To test for introgression between sibling species of horseshoe bat (Rhinolophus yunanensis and R. pearsoni) and two subspecies of the latter (R. p. pearsoni and R. p. chinensis), we sequenced two mtDNA and two ncDNA markers in individuals sampled from multiple localities within their overlapping ranges. The interspecific mtDNA gene tree corresponded to the expected taxonomic divisions, and coalescent‐based analyses suggested divergence occurred around 4 MYA. However, these relationships strongly conflicted with those recovered from two independent nuclear gene trees, in which R. yunanensis clustered with R. p. pearsoni to the exclusion of R. p. chinensis. This geographically widespread discordance is best explained by large‐scale historical introgression of ncDNA from R. yunanensis to R. pearsoni by male‐mediated exchange in mixed species colonies during Pleistocene glacial periods, when ranges may have contracted and overlapped more than at present. Further species tree–gene tree conflicts were detected between R. p. pearsoni and R. p. chinensis, also indicating past and/or current introgression in their overlapping regions. However, here the patterns point to asymmetric mtDNA introgression without ncDNA introgression. Analyses of coalescence times indicate this exchange has occurred subsequent to the divergence of these subspecies from their common ancestor. Our work highlights the importance of using multiple data sets for reconstructing phylogeographic histories and resolving taxonomic relationships.     

Coalescent theory for a completely random mating monoecious population

Consider a large random mating monoecious diploid population that has N individuals in each generation. Let us assume that at time 0 a random sample of ninfinity. It is then possible to obtain a generalization of coalescent theory for haploid populations if the distribution of G1 has a finite second moment and E[G(1)(3)]/N-->0 as N-->infinity.     

An information-theoretical approach to phylogeography

Data analysis in phylogeographic investigations is typically conducted in either a qualitative manner, or alternatively via the testing of null hypotheses. The former, where inferences about population processes are derived from geographical patterns of genetic variation, may be subject to confirmation bias and prone to overinterpretation. Testing the predictions of null hypotheses is arguably less prone to bias than qualitative approaches, but only if the tested hypotheses are biologically meaningful. As it is difficult to know a priori if this is the case, there is the general need for additional methodological approaches in phylogeographic research. Here, we explore an alternative method for analysing phylogeographic data that utilizes information theory to quantify the probability of multiple hypotheses given the data. We accomplish this by augmenting the model‐selection procedure implemented in ima with calculations of Akaike Information Criterion scores and model probabilities. We generate a ranking of 17 models each representing a set of historical evolutionary processes that may have contributed to the evolution of Plethodon idahoensis, and then quantify the relative strength of support for each hypothesis given the data using metrics borrowed from information theory. Our results suggest that two models have high probability given the data. Each of these models includes population divergence and estimates of ancestral θ that differ from estimates of descendent θ, inferences consistent with prior work in this system. However, the models disagree in that one includes migration as a parameter and one does not, suggesting that there are two regions of parameter space that produce model likelihoods that are similar in magnitude given our data. Results of a simulation study suggest that when data are simulated with migration, most of the optimal models include migration as a parameter, and further that when all of the shared polymorphism results from incomplete lineage sorting, most of the optimal models do not. The results could also indicate a lack of precision, which may be a product of the amount of data that we have collected. In any case, the information‐theoretic metrics that we have applied to the analysis of our data are statistically rigorous, as are hypothesis‐testing approaches, but move beyond the ‘reject/fail to reject’ dichotomy of conventional hypothesis testing in a manner that provides considerably more flexibility to researchers.     

Assessment of gene flow across a hybrid zone in red-tailed chipmunks (Tamias ruficaudus)

The role of hybridization in animal speciation is controversial and recent research has challenged the long-standing criterion of complete reproductive isolation to attain species status. The speciation-with-gene-flow model posits that the genome is semi-permeable and hybridization may be a phase in the process of divergence. Here, we apply these concepts to a previously identified zone of mtDNA introgression between the two strongly morphologically differentiated subspecies of red-tailed chipmunk ( Tamias ruficaudus ) in the US Inland Northwest. Using multilocus genotype data from the southern, older contact zone, we demonstrate that neutral gene flow is unusually low between the subspecies across the Lochsa River. This is geographically congruent with the discontinuity in bacular morphology, indicating that the cline of mitochondrial DNA (mtDNA) haplotypes is displaced. Furthermore, we elucidate the evolutionary forces responsible by testing hypotheses of lineage sorting and hybridization. We determined that introgressive hybridization is the cause of mtDNA/morphology incongruence because there are non-zero levels of migration and gene flow. Although our estimate of the age of the hybrid zone has wide credibility intervals, the hybridization events occurred in the Late Pleistocene and the divergence occurred in the Middle Pleistocene. Finally, we assessed substructure within and adjacent to the hybrid zone and found that the hybrid zone constitutes a set of populations that are genetically differentiated from parental sets of populations; therefore, hybridization in this system is not likely an evolutionary sink, but has generated novel combinations of genotypes.     

Phylogeny, divergence times and species limits of spiny lizards (Sceloporus magister species group) in western North American deserts and Baja California

The broad distribution of the Sceloporus magister species group (squamata: phrynosomatidae) throughout western North America provides an appropriate model for testing biogeographical hypotheses explaining the timing and origins of diversity across mainland deserts and the Baja California Peninsula. We inferred concordant phylogenetic trees describing the higher-level relationships within the magister group using 1.6 kb of mitochondrial DNA (mtDNA) and 1.7 kb of nuclear DNA data. These data provide strong support for the parallel divergence of lineages endemic to the Baja California Peninsula (S. zosteromus and the orcutti complex) in the form of two sequential divergence events at the base of the magister group phylogeny. A relaxed phylogenetic analysis of the mtDNA data using one fossil and one biogeographical constraint provides a chronology of these divergence events and evidence that further diversification within the Baja California clades occurred simultaneously, although patterns of geographical variation and speciation between clades differ. We resolved four major phylogeographical clades within S. magister that (i) provide a novel phylogenetic placement of the Chihuahuan Desert populations sister to the Mojave Desert; (ii) illustrate a mixed history for the Colorado Plateau that includes Mojave and Sonoran Desert components; and (iii) identify an area of overlap between the Mojave and Sonoran Desert clades near Yuma, Arizona. Estimates of bidirectional migration rates among populations of S. magister using four nuclear loci support strong asymmetries in gene flow among the major mtDNA clades. Based on the nonexclusivity of mtDNA haplotypes, nuclear gene flow among populations and wide zones of phenotypic intergradation, S. magister appears to represent a single geographically variable and widespread species.