Genetic Diversity and Demographic History in the Cactophilic Drosophila repleta Species Group (Diptera: Drosophilidae) in North America Inferred from Mitochondrial DNA Barcodes.

Genetic diversity in mitochondrial DNA barcodes, comprising a segment of the cytochrome c oxidase subunit I (COI) gene, was used to infer demographic histories in selected taxa of the cactophilic Drosophila repleta species group in North America. Haplotype and nucleotide diversities were determined in 16 taxa based on both previously published and new sequences. Haplotype diversity (h) differed dramatically in different taxa, varying from h = 0 in Drosophila eremophila, Drosophila hexastigma, and Drosophila bifurca to h = 0.99 in Drosophila hamatofila. Genetic diversity indices and sample sizes were sufficient to infer demographic histories from mismatch distribution analysis and Bayesian skyline plots for 9 taxa: Drosophila mojavensis baja, Drosophila mojavensis sonorensis, Drosophila arizonae, Drosophila aldrichi, D. hamatofila, Drosophila spenceri, Drosophila mainlandi, Drosophila mettleri, and Drosophila nigrospiracula. Evidence was found for both population expansions and relatively stable populations in these species. Demographic history varied dramatically in subspecies of D. mojavensis, showing a relatively stable population size over time in D. m. sonorensis from the mainland Sonoran Desert whereas a large population expansion was evident in D. m. baja from the Baja California Peninsula, providing support for the hypothesis that the split of sister species D. mojavensis and D. arizonae from a common ancestor occurred on the mainland rather than the peninsula as proposed by others. No evidence was found for a causal relationship between a stable or expanding population and host plant shifts from prickly-pear cactus to columnar cacti, which has occurred independently in many taxa of the repleta group.

Population Genetics of Overwintering Monarch Butterflies, Danaus plexippus (Linnaeus), from Central Mexico Inferred from Mitochondrial DNA and Microsatellite Markers.

Population genetic variation and demographic history in Danaus plexippus (L.), from Mexico were assessed based on analyses of mitochondrial cytochrome c oxidase subunit I (COI; 658 bp) and subunit II (COII; 503 bp) gene segments and 7 microsatellite loci. The sample of 133 individuals included both migratory monarchs, mainly from 4 overwintering sites within the Monarch Butterfly Biosphere Reserve (MBBR) in central Mexico (states of Michoacán and México), and a nonmigratory population from Irapuato, Guanajuato. Haplotype (h) and nucleotide (π) diversities were relatively low, averaging 0.466 and 0.00073, respectively, for COI, and 0.629 and 0.00245 for COII. Analysis of molecular variance of the COI data set, which included additional GenBank sequences from a nonmigratory Costa Rican population, showed significant population structure between Mexican migratory monarchs and nonmigratory monarchs from both Mexico and Costa Rica, suggesting limited gene flow between the 2 behaviorally distinct groups. Interestingly, while the COI haplotype frequencies of the nonmigratory populations differed from the migratory, they were similar to each other, despite the great physical distance between them. Microsatellite analyses, however, suggested a lack of structure between the 2 groups, possibly owing to the number of significant deviations from Hardy-Weinberg equilibrium resulting from heterzoygote deficiencies found for most of the loci. Estimates of demographic history of the combined migratory MBBR monarch population, based on the mismatch distribution and Bayesian skyline analyses of the concatenated COI and COII data set (n = 89) suggested a population expansion dating to the late Pleistocene (~35000-40000 years before present) followed by a stable effective female population size (Nef) of about 6 million over the last 10000 years.

Genetic diversity and population genetics of mosquitoes (Diptera: Culicidae: Culex spp.) from the Sonoran Desert of North America.

The population genetics and phylogenetic relationships of Culex mosquitoes inhabiting the Sonoran Desert region of North America were studied using mitochondrial DNA and microsatellite molecular markers. Phylogenetic analyses of mitochondrial cytochrome c oxidase subunit I (COI) from mosquitoes collected over a wide geographic area, including the Baja California peninsula, and mainland localities in southern Arizona, USA and Sonora, Mexico, showed several well-supported partitions corresponding to Cx. quinquefasciatus, Cx. tarsalis, and two unidentified species, Culex sp. 1 and sp. 2. Culex quinquefasciatus was found at all localities and was the most abundant species collected. Culex tarsalis was collected only at Tucson, Arizona and Guaymas, Sonora. The two unidentified species of Culex were most abundant at Navojoa in southern Sonora. Haplotype and nucleotide diversities in the COI gene segment were substantially lower in Cx. quinquefasciatus compared with the other three species. Analysis of molecular variance revealed little structure among seven populations of Cx. quinquefasciatus, whereas significant structure was found between the two populations of Cx. tarsalis. Evidence for an historical population expansion beginning in the Pleistocene was found for Cx. tarsalis. Possible explanations for the large differences in genetic diversity between Cx. quinquefasciatus and the other species of Culex are presented.

Population genetics and phylogenetic relationships of beetles (Coleoptera: Histeridae and Staphylinidae) from the Sonoran Desert associated with rotting columnar cacti.

Dozens of arthropod species are known to feed and breed in the necrotic tissues (rots) of columnar cacti in the Sonoran Desert. Because the necrotic patches are ephemeral, the associated arthropods must continually disperse to new cacti and therefore the populations of any given species are expected to show very little local genetic differentiation. While this has been found to be true for the cactophilic Drosophila, the evolutionary histories and characteristics of other arthropods inhabiting the same necrotic patches, especially the beetles, have yet to be examined. Here we used nucleotide sequence data from segments of the mitochondrial 16S rRNA and cytochrome c oxidase subunit I (COI) genes to examine population structure and demographic history of three sympatric beetle species (Coleoptera: Histeridae and Staphylinidae) collected on senita cactus (Lophocereus schottii) from six widely-separated localities on the Baja California peninsula of northwestern Mexico. Two histerids, Iliotona beyeri and Carcinops gilensis, and an unidentified staphylinid, Belonuchus sp., showed little or no population structure over a broad geographic area on the peninsula, consistent with the prediction that these beetles should show high dispersal ability. Demographic tests revealed varying levels of historical population expansion among the beetle species analyzed, which are discussed in light of their ecologies and concurrent biogeographic events. Additionally, phylogenetic analyses of COI sequences in Carcinops collected on a variety of columnar cacti from both peninsular and mainland Mexico localities revealed several species-level partitions, including a putative undescribed peninsular species that occurred sympatrically with C. gilensis on senita.

Phylogeography of the Cactophilic Drosophila and Other Arthropods Associated with Cactus Necroses in the Sonoran Desert.

Studies on the population genetics, phylogenetic relationships, systematics and evolution of arthropods that inhabit necrotic tissue of cacti in the Sonoran Desert of North America are reviewed. These studies have focused upon several species of insects (orders Diptera and Coleoptera) and arachnids (order Pseudoscorpiones). For most taxa studied, little genetic structure and high dispersal ability are found in populations inhabiting the mainland and Baja California peninsula regions of the Sonoran Desert, consistent with the availability of the rotting cactus microhabitat which is patchily distributed and ephemeral. There is evidence, however, that the Gulf of California, which bisects the Sonoran Desert, has played a role in limiting gene flow and promoting speciation in several taxa, including histerid beetles, whereas other taxa, especially Drosophila nigrospiracula and D. mettleri, apparently are able to freely cross the Gulf, probably by taking advantage of the Midriff Islands in the northern Gulf as dispersal "stepping stones". Genetic evidence has also been found for historical population expansions dating to the Pleistocene and late Pliocene in several taxa. Overall, these studies have provided important insights into how arthropods with different life history traits, but generally restricted to a necrotic cactus microhabitat, have evolved in an environmentally harsh and tectonically active region. In addition, they suggest some taxa for further, and more detailed, hypothesis driven studies of speciation.

Phylogenetic relationships of Sonoran Desert cactus beetles in the tribe Hololeptini (Coleoptera: Histeridae: Histerinae), with comments on the taxonomic status of Iliotona beyeri.

Nucleotide sequences from 16S rRNA and cytochrome c oxidase subunit I (COI) were used to examine phylogenetic relationships and evolution of beetles from the tribe Hololeptini (Coleoptera: Histeridae: Histerinae) that inhabit necrotic tissue of columnar cacti in the Sonoran Desert. Phylogenetic and morphological analyses revealed the presence of seven separate lineages, three representing species in the genus Iliotona, including I. beyeri stat. nov., and four species belonging to the genus Hololepta (sensu lato). The possible roles of historical vicariance and host plant associations on the evolution of the Hololeptini from the Sonoran Desert are discussed.

Mitochondrial DNA evidence for deep genetic divergences in allopatric populations of the rocky intertidal isopod Ligia occidentalis from the eastern Pacific.

Nucleotide sequences from the cytochrome c oxidase subunit I (COI) gene were used to test for genetic differentiation in the rocky intertidal isopod crustacean, Ligia occidentalis (Ligiidae), from the eastern Pacific. Phylogenetic analyses showed that individuals of L. occidentalis from southern California, USA to Manzanillo, Colima, Mexico partitioned into 15 highly-divergent clades. Mean Kimura 2-parameter (K2P) genetic distances among clades ranged from 13.2% to 26.7%. These values are similar to interspecific genetic distances found in a wide variety of crustaceans, including Ligia spp., suggesting that the taxon L. occidentalis represents a complex of cryptic species.

Genetic diversification and demographic history of the cactophilic pseudoscorpion Dinocheirus arizonensis from the Sonoran Desert.

Sequence data from a segment of the mitochondrial cytochrome c oxidase subunit I (COI) gene were used to examine phylogenetic relationships, estimate gene flow and infer demographic history of the cactophilic chernetid pseudoscorpion, Dinocheirus arizonensis (Banks), from the Sonoran Desert. Phylogenetic trees resolved two clades of D. arizonensis, one from mainland Sonora, Mexico and southern Arizona (clade I) and the other from the Baja California peninsula and southern Arizona (clade II). The two clades were separated by a mean genetic distance (d) of approximately 2.6%. Hierarchical analysis of molecular variance indicated highly significant population structuring in D. arizonensis (overall Phi(ST)=0.860; P<0.0001), with 80% of the genetic variation distributed among the two clades. Most pairwise comparisons of Phi(ST) among populations within each clade, however, were not significant. The results suggest that phoretic dispersal on vagile cactophilic insects such as the neriid cactus fly Odontoloxozus longicornis (Coquillett) provides sufficient gene flow to offset the accumulation of unique haplotypes within each clade of the non-vagile pseudoscorpion. Preliminary results on dispersal capability of O. longicornis were consistent with this conclusion. Tests designed to reconstruct demographic history from sequence data indicated that both clades of D. arizonensis, as well as O. longicornis, have experienced historical population expansions. Potential barriers to gene flow that may have led to genetic isolation and diversification in clades I and II of D. arizonensis are discussed.

Resurrection of the name Albula pacifica (Beebe, 1942) for the shafted bonefish (Albuliformes: Albulidae) from the eastern Pacific

The name Albula nemoptera (Fowler, 1911) is currently applied to the Shafted, or Threadfin, Bonefish (Albuliformes: Albulidae) inhabiting the tropical coastal waters of both the western Atlantic and eastern Pacific. In the present paper I provide a brief review of the taxonomy and nomenclature of A. nemoptera, and argue that the available morphological, biogeographical and molecular evidence supports resurrecting the name A. pacifica (Beebe, 1942) for the population of A. nemoptera from the eastern Pacific. Rev. Biol. Trop. 56 (2): 839-844. Epub 2008 June 30.

El nombre Albula nemoptera (Fowler, 1911) se aplica actualmente a las poblaciones del macabí de hebra (Albuliformes: Albulidae) de las aguas costeras tropicales del Atlántico Occidental y el Pacifico Oriental. En este artículo se presenta una revisión breve de la taxonomía y nomenclatura de A. nemoptera, y se sugiere que la evidencia morfológica, biogeográfica y molecular apoya el reestablecimiento del nombre A. pacifica (Beebe, 1942) para la población de A. nemoptera del Pacifico Oriental.

Resurrection of the name Albula pacifica (Beebe, 1942) for the shafted bonefish (Albuliformes: Albulidae) from the eastern Pacific.

The name Albula nemoptera (Fowler, 1911) is currently applied to the Shafted, or Threadfin, Bonefish (Albuliformes: Albulidae) inhabiting the tropical coastal waters of both the western Atlantic and eastern Pacific. In the present paper I provide a brief review of the taxonomy and nomenclature of A. nemoptera, and argue that the available morphological, biogeographical and molecular evidence supports resurrecting the name A. pacifica (Beebe, 1942) for the population ofA. nemoptera from the eastern Pacific.

Genetic differentiation and demographic history in Drosophila pachea from the Sonoran Desert.

Genetic variation at six microsatellite DNA loci and a segment of the mitochondrial cytochrome oxidase subunit I (COI) locus was used to estimate gene flow, population structure, and demographic history in the cactophilic Drosophila pachea from the Sonoran Desert of North America, a species that shows a strict association with its senita host cactus (genus Lophocereus). For microsatellite analyses, thirteen populations of D. pachea were sampled, five in mainland Mexico and the southwestern USA, and eight on the Baja California (Baja) peninsula, covering essentially the entire range of the species. Analysis of molecular variance (AMOVA) of microsatellite data revealed that populations from both the mainland and the Baja peninsula generally showed little structure, although there were a few exceptions, suggesting some local differentiation and restriction of gene flow within both regions. Pairwise comparisons of F(ST) among each of the mainland and Baja populations showed evidence of both panmixia and population subdivision. AMOVA performed on grouped populations from both the mainland and Baja, however, revealed significant partitioning of genetic variation among the two regions, but no partitioning among localities within each region. Bayesian skyline analyses of the COI data set, consisting of four mainland and seven peninsular populations, revealed population expansions dating to the Pleistocene or late Pliocene in D. pachea from both regions, although regional differences were seen in the estimated timing of the expansions and in changes in effective population size over time.

Inhibition of alcohol dehydrogenase after 2-propanol exposure in different geographic races of Drosophila mojavensis: lack of evidence for selection at the Adh-2 locus.

High frequencies of the fast allele of alcohol dehydrogenase-2 (Adh-2F) are found in populations of Drosophila mojavensis that inhabit the Baja California peninsula (race BII) whereas the slow allele (Adh-2S) predominates at most other localities within the species' geographic range. Race BII flies utilize necrotic tissue of pitaya agria cactus (Stenocereus gummosus) which contains high levels of 2-propanol, whereas flies from most other localities utilize different cactus hosts in which 2-propanol levels are low. To test if 2-propanol acts as a selective force on Adh-2 genotype, or whether some other yet undetermined genetic factor is responsible, mature males of D. mojavensis lines derived from the Grand Canyon (race A) and Santa Catalina Island (race C), each with individuals homozygous for Adh-2F and Adh-2S, were exposed to 2-propanol for 24 h and ADH-2 specific activity was then determined on each genotype. Flies from five other localities homozygous for either the fast or slow allele also were examined. Results for all reported races of D. mojavensis were obtained. 2-propanol exposure inhibited ADH-2 specific activity in both genotypes from all localities, but inhibition was significantly less in two populations of race BII flies homozygous for Adh-2F. When F/F and S/S genotypes in flies from the same locality were compared, both genotypes showed high 2-propanol inhibition that was not statistically different, indicating that the F/F genotype alone does not provide a benefit against the inhibitory effects of 2-propanol. ADH-1 activity in female ovaries was inhibited less by 2-propanol than ADH-2. These results do not support the hypothesis that 2-propanol acts as a selective factor favoring the Adh-2F allele.

Linking behavioral ecology with population genetics: insights from Drosophila nigrospiracula.

Although Drosophila species provide important model systems for evolutionary biology, the ecologies and natural histories of most species are insufficiently characterized to permit predictions with respect to issues such as population genetic structure. A notable exception is the group of cactophilic Drosophila endemic to the Sonoran Desert of North America. One of these species, D. nigrospiracula, exhibits no population subdivision anywhere in its range. Here we present evidence suggesting that the timing of mating in relation to dispersal contributes to the panmixia observed in this species.

Phylogenetic relationships of elopomorph fishes inferred from mitochondrial ribosomal DNA sequences.

The superorder Elopomorpha, a grouping which includes all teleost fishes that possess a specialized leptocephalous larva [true eels (Anguilliformes), gulpers and bobtail snipe eels (Saccopharyngiformes), bonefishes, spiny eels, and halosaurs (Albuliformes, including Notacanthiformes), ladyfishes and tarpons (Elopiformes, including Megalopiformes)] comprises >800 species for which phylogenetic relationships are poorly understood. In the present study, we analyzed mitochondrial DNA sequences in segments of the 12S and 16S rRNA genes in 33 elopomorph taxa encompassing all of the previously proposed orders, and 9 of the 15 currently recognized families of the Anguilliformes, as well as outgroup representatives from the superorders Osteoglossomorpha (nine species) and Clupeomorpha (three species), to develop phylogenetic hypotheses based on distance and parsimony methods. Both methods failed to support the monophyly of the Elopomorpha, casting doubt on the validity of the leptocephalus as an elopomorph synapomorphy. The orders Elopiformes, Albuliformes, and Anguilliformes, however, were resolved as monophyletic assemblages. Parsimony analysis supported the separation of the Anguilliformes into two groups (primitive and advanced) based on the presence of divided versus fused frontal bones. In addition, the molecular data indicated a close affinity of the anguilliform Thalassenchelys coheni (incertae sedis), known only from the leptocephalus, with the family Serrivomeridae. The implications of these data as regards the evolution of the elopomorph assemblage are discussed.

Induction of suppressed ADH activity in Drosophila pachea exposed to different alcohols.

Laboratory-reared males of the cactophilic Drosophila pachea exhibit a spontaneous and sex-specific suppression of alcohol dehydrogenase (ADH) activity within 4 days after eclosion. A lack of ADH activity also is usually seen in wild-caught males, although relatively high activity is always seen in female flies. In the present study we examined the effectiveness of different alcohols and related compounds, including several found naturally in necroses of the host cactus, to induce suppressed ADH activity in wild males of D. pachea and to serve as enzyme substrates. The primary alcohols (methanol, ethanol, 1-propanol, 1-butanol, and 1-pentanol), and the secondary alcohols (2-propanol and 2-butanol), each induced activity after 24 h exposure, although to different degrees. 1,2-Propanediol was usually effective as an inducer, but 2,3-butanediol usually was ineffective. Little or no induction was seen with 1-octanol, 2-pentanol, 3-methyl-1-butanol, 3-hydroxy-2-butanone, or acetaldehyde. Although the compounds tested varied in their ability to function as ADH substrates, methanol was the only alcohol that showed no activity staining. Ethanol induction of ADH activity was apparent after 3-6 h exposure and induced activity decreased dramatically within 1 week of flies being placed in an alcohol-free environment. Ethanol exposure did not induce ADH in adult female D. pachea, or in adult males and females of D. acutilabella in which control males show reduced ADH activity compared to females. The implications of the loss of ADH activity in adult males of D. pachea, as they relate to feeding ecology and fitness, are discussed.

Flies across the water: genetic differentiation and reproductive isolation in allopatric desert Drosophila.

Between sister species of Drosophila, both pre- and postzygotic reproductive isolation commonly appear by the time a Nei's genetic distance of 0.5 is observed. The degree of genetic differentiation present when allopatric populations of the same Drosophila species exhibit incipient reproductive isolation has not been systematically investigated. Here we compare the relationship between genetic differentiation and pre- and postzygotic isolation among allopatric populations of three cactophilic desert Drosophila: D. mettleri, D. nigrospiracula, and D. mojavensis. The range of all three is interrupted by the Gulf of California, while two species, D. mettleri and D. mojavensis, have additional allopatric populations residing on distant Santa Catalina Island, off the coast of southern California. Significant population structure exists within all three species, but only for allopatric populations of D. mojavensis is significant isolation at the prezygotic level observed. The genetic distances for the relevant populations of D. mojavensis were in the range of 0.12, similar to that for D. mettleri whose greatest D = 0.11 was unassociated with any form of isolation. These observations suggest further investigations of Drosophila populations with genetic distances in this range be undertaken to identify any potential patterns in the relationship between degree of genetic differentiation and the appearance of pre- and/or postzygotic isolation.

Identification, structural analysis and function of hyaluronan in developing fish larvae (leptocephali).

Hyaluronan (HA) has been identified as the principal glycosaminoglycan (CAG) in the highly hydrated, extracellular body matrix of the larval stage (leptocephalus) of seven species of true eels (Teleostei: Elopomorpha: Anguilliformes) and the ladyfish Elops saurus (Elopiformes), and was found as a minor GAG component in the bonefish Albula sp. (Albuliformes). Identification was based on: (1) HPLC separation of unsaturated disaccharides derived from chondroitinase ABC digests of whole-body GAG extracts; (2) 1H NMR analyses of native GAG polymers; and (3) degradation of GAG extracts by Streptomyces hyaluronan lyase. The unsaturated disaccharide 2-acetamido-2-deoxy-3-O-(beta-D-gluco-4-enepyranosyluronic acid)-D-glucose (DeltaDi-HA) accounted for 92.4-99.8% of the total disaccharides in chondroitinase digests. Trace amounts of unsaturated disaccharides of chondroitin sulfate were also present. Two-dimensional gCOSY spectra of the native HA polymer were similar for all species. Proton assignments for the HA disaccharide repeat (GlcAbeta1-3GlcNAcbeta1-4) in D(2)O, based on gCOSY, DQF-COSY and TOCSY analyses for the eel Ahlia egmontis, were concordant with published chemical shifts for HA oligosaccharides. In addition to its presumed role in maintaining the structural integrity and hydration of the gelatinous body of the leptocephalus, HA is postulated to function as a storage polysaccharide in those species in which it is the predominant GAG.

DIFFERENTIAL SURVIVAL OF SEXUAL AND ASEXUAL POECILIOPSIS DURING ENVIRONMENTAL STRESS.

According to the Frozen Niche-Variation model, coexisting clones of an asexual species can freeze and faithfully replicate ecologically relevant genetic variability that segregates in the sexual ancestors. The present experiments with fish of the genus Poeciliopsis provide further evidence in support of this model. Sexual and clonal forms of Poeciliopsis live in the desert streams of Sonora, Mexico, and are exposed to environmental extremes ranging from flash floods to hot, desiccating, residual pools. We examined coexisting members of the monacha complex to see whether the fish types differed with respect to survival during stress and swimming endurance in an artificial flume. The two coexisting clones of the triploid gynogenetic fish P. 2 monacha-lucida differed dramatically: clone MML/II had the best survival during heat and cold stress and the worst survival during hypoxic stress, whereas clone MML/I had the best survival during hypoxic stress and the worst during heat stress. Poeciliopsis monacha, the sexual species with which these clones coexist, had intermediate survival during heat and hypoxic stress and very poor swimming endurance in the flume. The physiological differences seen in this study are consistent with the Frozen Niche-Variation model and provide some insights into environmental factors that affect the distribution and abundance of these fish.

BALANCING SELECTION IN A DESERT STREAM-DWELLING FISH, POECILIOPSIS MONACHA.

The desert stream-dwelling fish Poeciliopsis monacha is exposed to extreme seasonal and spatial variation in physical stresses. We examined four diallelic gene loci (Ldh-1, Idh-2, Pgd, and Ck-A) in P. monacha and tested whether genotypes were associated with differential survival of individuals exposed to acute stress. For each locus, the common allele was associated with higher survival during heat and hypoxic stress, whereas the alternate allele was associated with higher survival during cold stress. In most cases, survival of heterozygotes was intermediate and they exhibited less variance in survival than corresponding homozygotes. Identification of substantial linkage disequilibrium in these fish confounds our ability to discern whether the allozymes are the direct targets of selection, or if they just mark chromosomal regions that contain the true modifiers of survival. Nevertheless, the present results clearly identified balancing processes that can serve to stabilize genetic polymorphism in this species.