Concordance of genetic divergence among sockeye salmon populations at allozyme, nuclear DNA, and mitochondrial DNA markers

Abstract.— We examined genetic variation at 21 polymorphic allozyme loci, 15 nuclear DNA loci, and mitochondrial DNA in four spawning populations of sockeye salmon ( Oncorhynchus nerka ) from Cook Inlet, Alaska, to test for differences in the patterns of divergence among different types of markers. We were specifically interested in testing the suggestion that natural selection at allozyme loci compromises the effectiveness of these markers for describing the amount and patterns of gene flow among populations. We found concordance among markers in the amount of genetic variation within and among populations, with the striking exception of one allozyme locus ( sAH ), which exhibited more than three times the amount of among-population differentiation as other loci. A consideration of reports of discordance between allozymes and other loci indicates that these differences usually result from one or two exceptional loci. We conclude that it is important to examine many loci when estimating genetic differentiation to infer historical amounts of gene flow and patterns of genetic exchange among populations. It is less important whether those loci are allozymes or nuclear DNA markers.     

Restricted gene flow and incipient speciation in disjunct Pacific Ocean and Sea of Cortez populations of a reef fish species, Girella nigricans

Abstract.— Population disjunctions have been proposed to play an important role in speciation processes. In this study, we have examined the possible role of the Pacific Ocean-Sea of Cortez disjunction as a contributing factor to cryptic speciation in a reef fish, the opaleye, Girella nigricans . Mitochondrial control region (D-loop) sequences (380 bp) of 117 individuals completely separated opaleye populations from the Pacific Ocean and the Sea of Cortez. Although opaleye exhibit pelagic larval stages that remain in the water column for several months, gene flow between the Pacific Ocean and the Sea of Cortez was found to be extremely limited ( F_ST = 0.84, Nm = 0.10). Whereas limited gene flow and reciprocal monophyly suggest that the observed physical and genetic disjunction are potentially contributing to the incipient speciation of Pacific and Sea of Cortez opaleye, moderate levels of D-loop sequence divergence (3.3%) and the absence of fixed allozyme markers challenge this idea. Pacific Coast populations also exhibited restricted gene flow levels ( F_ST = 0.25, Nm = 1.49) across Punta Eugenia, a recognized oceanographic boundary along the Baja California coast. Thus, opaleye individuals grouped into three clades: one clade in the Sea of Cortez, one Pacific clade south of Punta Eugenia, and one Pacific clade north of Punta Eugenia. Future work in this region will determine if our results can be generalized to other disjunct populations.     

Colonization and diversification of the species Brachyderes rugatus (Coleoptera) on the Canary Islands: evidence from mitochondrial DNA COII gene sequences

Abstract.— The genus Brachyderes Schönherr (Coleoptera: Curculionidae) is represented by the species B. rugatus Wollaston on the Canary Islands, with one subspecies on each of the islands of Gran Canaria, Tenerife, La Palma, and El Hierro. These four subspecies are associated with the endemic pine tree Pinus canariensis , and their distributions are broadly coincident. Eighty-eight individual Canarian Brachyderes , sampled from across the distributions of each subspecies, have been sequenced for 570 bp of the mitochondrial DNA (mtDNA) cytochrome oxidase II gene (COII). No mitotypes are shared among islands. Both maximum-likelihood and distance-based phylogenetic analyses have shown that: Tenerife is composed of a single monophyletic clade of mitotypes, El Hierro is composed of a single monophyletic clade occurring within a larger clade comprising all the La Palma mitotypes, and the mitotypes of these three islands form a monophyletic group distinct from Gran Canaria. New methods for estimating divergence times without the assumption of rate constancy have been used to reconstruct the direction and approximate timing of colonizations among the islands. Colonization has occurred from older to progressionally younger islands, and these colonizations are estimated to have occurred less than 2.6 million years ago, although the timing of the initial colonization of the archipelago is not discernable. New methods for the estimation of diversification rates that use branching times as the analyzed variable have been applied to each island fauna. Hypothesized effects of different levels of recent volcanism among islands were not apparent. All islands exhibit a gradually decreasing rate of genetic diversification that is marked by periodic sudden changes in rate.     

Interpreting colonization of the Calathus (Coleoptera: Carabidae) on the Canary Islands and Madeira through the application of the parametric bootstrap

The Canary Islands have proven to be an interesting archipelago for the phylogeographic study of colonization and diversification with a number of recent studies reporting evolutionary patterns and processes across a diversity of floral and faunal groups. The Canary Islands differ from the Hawaiian and Galapagos Islands by their close proximity to a continental land mass, being 110 km from the northwestern coast of Africa. This close proximity to a continent obviously increases the potential for colonization, and it can be expected that at the level of the genus some groups will be the result of more than one colonization. In this study we investigate the phylogeography of a group of carabid beetles from the genus Calathus on the Canary Islands and Madeira, located 450 km to the north of the Canaries and 650 km from the continent. The Calathus are well represented on these islands with a total of 29 species, and on the continent there are many more. Mitochondrial cytochrome oxidase I and II sequence data has been used to identify the phylogenetic relationships among the island species and a selection of continental species. Specific hypotheses of monophyly for the island fauna are tested with parametric bootstrap analysis. Data suggest that the Canary Islands have been colonized three times and Madeira twice. Four of these colonizations are of continental origin, but it is possible that one Madeiran clade may be monophyletic with a Canarian clade. The Calathus faunas of Tenerife and Madeira are recent in origin, similar to patterns previously reported for La Gomera, El Hierro, and Gran Canaria.     

Mitochondrial DNA phylogeography of the polytypic North American rat snake (Elaphe obsoleta): a critique of the subspecies concept

Subspecies have been considered artificial subdivisions of species, pattern classes, or incipient species. However, with more data and modern phylogenetic techniques, some subspecies may be found to represent true species. Mitochondrial DNA analysis of the polytypic snake, Elaphe obsoleta, yields well-supported clades that do not conform to any of the currently accepted subspecies. Complete nucleotide sequences of the cytochrome b gene and the mitochondrial control region produced robust maximum-parsimony and maximum-likelihood trees that do not differ statistically. Both trees were significantly shorter than a most parsimonious tree in which each subspecies was constrained to be monophyletic. Thus, the subspecies of E. obsoleta do not represent distinct genetic lineages. Instead, the evidence points to three well-supported mitochondrial DNA clades confined to particular geographic areas in the eastern United States. This research underscores the potential problems of recognizing subspecies based on one or a few characters.     

Identification of amino acid residues of GABA(A) receptor subunits contributing to the formation and affinity of the tert-butylbicyclophosphorothionate binding site

A chimeric GABA(A) receptor subunit was constructed that contained the beta3 sequence from the N-terminus to the first two amino acids of the second transmembrane (TM2) domain. The remaining part of this chimera had the sequence of the alpha1 subunit. On co-expression with alpha1 subunits, this chimera was able to form heterooligomeric channels that were open in the absence of GABA. Picrotoxin and tert-butylbicyclophosphorothionate (TBPS) were able to block these channels with low potency. These channels exhibited high-affinity [3H]muscimol but no high-affinity [35S]TBPS binding sites. Introduction of V251, A252, and L253 of the beta3 subunit into the chimera resulted in the formation of closed channels that could be opened by GABA. The introduction of A252 and L253 of the beta3 subunit into this chimera was sufficient to reconstitute the specific high-affinity [35S]TBPS binding site in receptors composed of the chimera and alpha1 subunits. Replacement of other amino acids of the TM2 region of the chimera with corresponding amino acids of the beta3 subunit modulated the affinity of this [35S]TBPS binding site. Results obtained provide important information on the structure-function relationship of GABA(A) receptors.     

Inactivation of Mitochondrial Permeability Transition Pore by Octylguanidine and Octylamine

Mitochondrial permeability transition occurs through a Ca²⁺-dependent opening of atransmembrane pore, whose identity has been attributed to that of the adenine nucleotide translocase(ANT). In this work, we induced permeability transition by adding 0.5 M carboxyatractyloside.The process was evaluated analyzing Ca²⁺ efflux, a drop in transmembrane electric gradient,and swelling. We found that the amphiphyllic cations octylguanidine and octylamine, at theconcentration of 100 M, inhibited, almost completely, nonspecific membrane permeability.Hexylguanidine, hexylamine, as well as guanidine chloride and hydroxylamine failed to doso. The inhibition was reversed after the addition of 40 mM Li⁺, Na⁺ K⁺,Rb⁺, or Cs⁺; K⁺ wasthe most effective. We propose that the positive charge of the amines interact with negativecharges of membrane proteins, more likely the ADP/ATP carrier, while the alkyl chain penetratesinto the hydrophobic milieu of the inner membrane, fixing the reagent.     

Non-geographically based population structure of South Pacific sperm whales: dialects, fluke-markings and genetics

1. This study addresses the issue of structure in sperm whale ( Physeter macrocephalus Linnaeus) populations and whether it is geographically based.
2. During a survey around the South Pacific Ocean, we collected sloughed skin for genetic analyses, recorded coda vocalizations, and photographed fluke markings.
3. Groups of female and immature sperm whales had characteristic mitochondrial haplotypes, coda repertoires, and fluke-mark patterns, but there was no clear geographical structure in any of these attributes.
4. However, similarities of coda repertoire and mitochondrial haplotype distribution were significantly correlated among pairs of groups in a manner that was not geographically based. There was also a significant canonical correlation coefficient between coda repertoire and fluke-mark patterns.
5. These results suggest that attributes (such as vocal repertoire and techniques of predator defence) which are acquired matrilineally, and probably culturally, are conserved during the fission and dispersal of groups.     

MITOCHONDRIAL PHYLOGEOGRAPHY OF THE LAND SNAIL ALBINARIA IN CRETE: LONG-TERM GEOLOGICAL AND SHORT-TERM VICARIANCE EFFECTS

The land snail genus Albinaria exhibits an extreme degree of morphological differentiation in Greece, especially in the island of Crete. Twenty-six representatives of 17 nominal species and a suspected hybrid were examined by sequence analysis of a PCR-amplified mitochondrial DNA fragment of the large rRNA subunit gene. Maximum parsimony and neighbor-joining phylogenetic analyses demonstrate a complex pattern of speciation and differentiation and suggest that Albinaria species from Crete belong to at least three distinct monophyletic groups, which, however, are not monophyletic with reference to the genus as a whole. There is considerable variation of genetic distance within and among “species” and groups. The revealed phylogenetic relations do not correlate well with current taxonomy, but exhibit biogeographical coherence. Certain small- and large-scale vicariance events can be traced, although dispersal and parapatric speciation may also be present. Our analysis suggests that there was an early and rapid differentiation of Albinaria groups across the whole of the range followed by local speciation events within confined geographical areas.     

Activation of Shaker Potassium Channels : III. An Activation Gating Model for Wild-Type and V2 Mutant Channels

A functional kinetic model is developed to describe the activation gating process of the Shaker potassium channel. The modeling in this paper is constrained by measurements described in the preceding two papers, including macroscopic ionic and gating currents and single channel ionic currents. These data were obtained from the normally activating wild-type channel as well as a mutant channel V2, in which the leucine at position 382 has been mutated to a valine. Different classes of models that incorporate Shaker''s symmetrical tetrameric structure are systematically examined. Many simple gating models are clearly inadequate, but a model that can account for all of the qualitative features of the data has the channel open after its four subunits undergo three transitions in sequence, and two final transitions that reflect the concerted action of the four subunits. In this model, which we call Scheme 3+2′, the channel can also close to several states that are not part of the activation path. Channel opening involves a large total charge movement (10.8 e₀), which is distributed among a large number of small steps each with rather small charge movements (between 0.6 and 1.05 e₀). The final two transitions are different from earlier steps by having slow backward rates. These steps confer a cooperative mechanism of channel opening at Shaker''s activation voltages. In the context of Scheme 3+2′, significant effects of the V2 mutation are limited to the backward rates of the final two transitions, implying that L382 plays an important role in the conformational stability of the final two states.