Frank E. Anderson

Phylogenetic inference in Rafflesiales: the influence of rate heterogeneity and horizontal gene transfer

BackgroundThe phylogenetic relationships among the holoparasites of Rafflesiales have remained enigmatic for over a century. Recent molecular phylogenetic studies using the mitochondrial matR gene placed Rafflesia, Rhizanthes and Sapria (Rafflesiaceae s. str.) in the angiosperm order Malpighiales and Mitrastema (Mitrastemonaceae) in Ericales. These phylogenetic studies did not, however, sample two additional groups traditionally classified within Rafflesiales (Apodantheaceae and Cytinaceae). Here we provide molecular phylogenetic evidence using DNA sequence data from mitochondrial and nuclear genes for representatives of all genera in Rafflesiales.ResultsOur analyses indicate that the phylogenetic affinities of the large-flowered clade and Mitrastema, ascertained using mitochondrial matR, are congruent with results from nuclear SSU rDNA when these data are analyzed using maximum likelihood and Bayesian methods. The relationship of Cytinaceae to Malvales was recovered in all analyses. Relationships between Apodanthaceae and photosynthetic angiosperms varied depending upon the data partition: Malvales (3-gene), Cucurbitales (matR) or Fabales (atp1). The latter incongruencies suggest that horizontal gene transfer (HGT) may be affecting the mitochondrial gene topologies. The lack of association between Mitrastema and Ericales using atp1 is suggestive of HGT, but greater sampling within eudicots is needed to test this hypothesis further.ConclusionsRafflesiales are not monophyletic but composed of three or four independent lineages (families): Rafflesiaceae, Mitrastemonaceae, Apodanthaceae and Cytinaceae. Long-branch attraction appears to be misleading parsimony analyses of nuclear small-subunit rDNA data, but model-based methods (maximum likelihood and Bayesian analyses) recover a topology that is congruent with the mitochondrial matR gene tree, thus providing compelling evidence for organismal relationships. Horizontal gene transfer appears to be influencing only some taxa and some mitochondrial genes, thus indicating that the process is acting at the single gene (not whole genome) level.

Complete Mitochondrial Genome Sequences and the Phylogeny of Cranes (Gruiformes: Gruidae)

ABSTRACT. We estimated phylogenetic relationships among all 15 extant species of cranes in the gruiform family Gruidae from complete sequences of their mitochondrial genomes. The gene order of crane mitochondrial genomes corresponds to that of the chicken and present few structural novelties compared with previously described birds. Sequences of the control region, particularly domains I and III, are highly divergent among species and include tandem repeats, duplications, and numerous indels. Phylogenetic analyses confirmed the well-established, reciprocal monophyly of clades Balearicinae (crowned cranes) and Gruinae (anatomically derived cranes), as well as previously identified lineages within Gruinae: Leucogeranus and the species groups Anthropoides, Canadensis, Antigone, and Americana. As in previous molecular phylogenies, Leucogeranus is resolved as sister to all other gruines. In addition, the Sandhill Crane (Grus canadensis) is resolved as sister to the Antigone species group, resulting in a Pacific Rim clade that has not previously been suggested. Only relationships among the Anthropoides, Americana, and Pacific Rim groups remain unresolved in our analyses. The crane fossil record provides reasonable calibration points for the most recent common ancestor of Gruinae (Middle Miocene) and the minimum age of Grus americana (Late Pliocene). Bayesian estimates of divergence dates from mitochondrial DNA sequences suggest that balearicines and gruines separated in the late Oligocene and that radiations of living species within these clades took place in the Neogene.

Phylogeography of the pharaoh cuttle Sepia pharaonis based on partial mitochondrial 16S sequence data

The pharaoh cuttle Sepiapharaonis Ehrenberg, 1831 (Mollusca: Cephalopoda: Sepiida) is a broadly distributed species of substantial fisheries importance found from east Africa to southern Japan. Little is known about S. pharaonis phylogeography, but evidence from morphology and reproductive biology suggests that Sepiapharaonis is actually a complex of at least three species. To evaluate this possibility, we collected tissue samples from Sepia pharaonis from throughout its range. Phylogenetic analyses of partial mitochondrial 16S sequences from these samples reveal five distinct clades: a Gulf of Aden/Red Sea clade, a northern Australia clade, a Persian Gulf/Arabian Sea clade, a western Pacific clade (Gulf of Thailand and Taiwan) and an India/Andaman Sea clade. Phylogenetic analyses including several Sepia species show that S. pharaonis sensu lato may not be monophyletic. We suggest that “S. pharaonis” may consist of up to five species, but additional data will be required to fully clarify relationships within the S. pharaonis complex.

Molecular evidence for co-occurring cryptic lineages within the Sepioteuthis cf. lessoniana species complex in the Indian and Indo-West Pacific Oceans

AbstractThe big-fin reef squid, Sepioteuthis cf. lessoniana (Lesson 1930), is an important commodity species within artisanal and near-shore fisheries in the Indian and Indo-Pacific regions. While there has been some genetic and physical evidence that supports the existence of a species complex within S. cf. lessoniana, these studies have been extremely limited in scope geographically. To clarify the extent of cryptic diversity within S. cf. lessoniana, this study examines phylogenetic relationships using mitochondrial genes (cytochrome oxidase c, 16s ribosomal RNA) and nuclear genes (rhodopsin, octopine dehydrogenase) from nearly 400 individuals sampled from throughout the Indian, Indo-Pacific, and Pacific Ocean portions of the range of this species. Phylogenetic analyses using maximum likelihood methods and Bayesian inference identified three distinct lineages with no clear geographic delineations or morphological discriminations. Phylogeographic structure analysis showed high levels of genetic connectivity in the most widespread lineage, lineage C and low levels of connectivity in lineage B. This study provides significant phylogenetic evidence for cryptic lineages within this complex and confirms that cryptic lineages of S. cf. lessoniana occur in sympatry at both small and large spatial scales. Furthermore, it suggests that two closely related co-occurring cryptic lineages have pronounced differences in population structure, implying that underlying differences in ecology and/or life history may facilitate co-occurrence. Further studies are needed to assess the range and extent of cryptic speciation throughout the distribution of this complex. This information is extremely useful as a starting point for future studies exploring the evolution of diversity within Sepioteuthis and can be used to guide fisheries management efforts.

Ancestral state reconstruction for Dendroctonus bark beetles: evolution of a tree killer.

ABSTRACT While most bark beetles attack only dead or weakened trees, many species in the genus Dendroctonus have the ability to kill healthy conifers through mass attack of the host tree, and can exhibit devastating outbreaks. Other species in this group are able to successfully colonize trees in small numbers without killing the host. We reconstruct the evolution of these ecological and life history traits, first classifying the extant Dendroctonus species by attack type (mass or few), outbreaks (yes or no), host genus (Pinus and others), location of attacks on the tree (bole, base, etc.), whether the host is killed (yes or no), and if the larvae are gregarious or have individual galleries (yes or no). We then estimated a molecular phylogeny for a data set of cytochrome oxidase I sequences sampled from nearly all Dendroctonus species, and used this phylogeny to reconstruct the ancestral state at various nodes on the tree, employing maximum parsimony, maximum likelihood, and Bayesian methods. Our reconstructions suggest that extant Dendroctonus species likely evolved from an ancestor that killed host pines through mass attack of the bole, had individual larvae, and exhibited outbreaks. The ability to colonize a host tree in small numbers (as well as gregarious larvae and attacks at the tree base) apparently evolved later, possibly as two separate events in different clades. It is likely that tree mortality and outbreaks have been continuing features of the interaction between conifers and Dendroctonus bark beetles.

Population genetics of the carinate pillsnail, Euchemotrema hubrichti: genetic structure on a small spatial scale

Euchemotrema hubrichti (Pilsbry HA (1940) Volume 1, Part 2. Monographs of the Academy of Natural Sciences, Philadelphia, 3, I-VI, 2, 575–994, I-IX) is a polygyrid land snail known only from the Larue Pine Hills region of southwestern Illinois, USA. Despite the restricted range of the species, observations in the field suggested that patterns of genetic variation within E. hubrichti might show geographic structure. To assess the dispersal potential of E. hubrichti, a mark-recapture experiment was performed at two sites <100 meters apart. To evaluate the geographic distribution of genetic variation, a region of the mitochondrial cytochrome c oxidase subunit I gene was sequenced from 53 snails collected from sites spanning the species range. Mark-recapture experiments suggested that population sizes at two sites were low and migration between sites was not detected. AMOVA and nested clade analysis (NCA) revealed significant genetic structure among sites. Two sites in particular appeared to be isolated from the others based on nested clade analysis. AMOVA also detected significant genetic differentiation among sites, but partitioning the data into two groups (populations 1 and 2) based on the NCA results did not explain a significant amount of genetic variation. Coalescent methods suggested that population sizes and migration rates for populations 1 and 2 are unequal. These patterns are likely due to the low dispersal ability of E. hubrichti and patchiness of preferred E. hubrichti habitat rather than an ancient vicariant event. These preliminary findings have implications both for the conservation of this species and for the population genetics of any spatially restricted endemic species with low dispersal ability.

Mitochondrial DNA analysis of the bark beetle predator Thanasimus dubius F. (Coleoptera: Cleridae) reveals regional genetic differentiation.

The checkered beetle, Thanasimus dubius F., is an important predator of scolytid bark beetles that attack conifers. Relatively few studies exist that have addressed the population genetics of predatory beetles, especially those with potential as biological control agents. This study was conducted to investigate the population genetics of T. dubius across a large part of its range in the eastern United States. A 464‐base pair portion of the mitochondrial cytochrome c oxidase subunit I was sequenced for 85 individuals resulting in 60 haplotypes. Analysis of molecular variance was conducted on the resulting haplotypes for all populations and as a hierarchical analysis between populations defined as broad‐scale northern and southern groups. Results indicate a significant overall ΦST = 0.220 (P < 0.001) for all populations with the hierarchical analysis revealing that this significant ΦST is due to structuring of the populations between northern and southern regions (ΦCT = 0.388, P < 0.009). The observed genetic structure is possibly due to the discontinuous distribution of pine trees, which act as hosts for the prey of T. dubius, which has occurred historically in the central region of the United States that has been covered by prairie.

Lights out: the evolution of bacterial bioluminescence in Loliginidae

Representatives of several metazoan clades engage in symbiotic interactions with bioluminescent bacteria, but the evolution and maintenance of these interactions remain poorly understood. Uroteuthis is a genus of loliginid squid (Cephalopoda: Loliginidae) characterized by paired ventral photophores (light organs) housing bioluminescent bacteria. While previous phylogenetic studies have suggested that Uroteuthis is closely related to Loliolus, a genus of non-bioluminescent species, this relationship remains unresolved. To illuminate Uroteuthis and Loliolus phylogeny and its implications for the evolution of bioluminescence in Loliginidae, we generated sequences from two mitochondrial genes from Uroteuthis specimens sampled from several sites in the Indian and western Pacific Oceans. We combined these data with data from GenBank, analyzed the concatenated data set using maximum likelihood and Bayesian methods, and reconstructed the evolution of bacterial bioluminescence on the resulting phylogenies. Our analyses support the hypothesis that Uroteuthis is paraphyletic with respect to Loliolus. Furthermore, our reconstructions suggest that the symbiosis between loliginid squid and bioluminescent bacteria evolved once in the ancestor of Loliolini (the clade comprising Uroteuthis and Loliolus), but was subsequently lost in the ancestor of Loliolus. These findings could have profound implications for our understanding of the evolution of symbiotic bioluminescence in squid.

Molecular phylogeny, evolution of shell shape, and DNA barcoding in Polygyridae (Gastropoda: Pulmonata), an endemic North American clade of land snails

Abstract: A hypothesis of relationships among subfamilies, tribes, genera, and species of Polygyridae was established by Ken Emberton in 1995, using shell, behavioral, allozyme, and soft anatomical characters. We tested this hypothesis using four mitochondrial and two nuclear loci. We present data from 418 polygyrid individuals sequenced for one to six loci, including 110 named species (out of 294 nominal taxa) from 21 of the 24 recognized genera. We carried out phylogenetic and DNA barcoding analyses to examine relationships at the family, genus, and species-level. In our analyses, the subfamilies are not supported as monophyletic groups. The tribes Mesodontini, Ashmunellini and Vespericolini were recovered as monophyletic, while all other tribes were paraphyletic. Regardless of analysis method, we found a close, well-supported relationship between Mesodontini and Triodopsini, two tribes that were distantly related in Embertons hypothesis. Most genera were recovered as monophyletic with the notable exceptions of Cryptomastix Pilsbry, 1839, Mesodon Rafinesque in Férussac, 1821, and Neohelix von Ihering, 1892. Of the species for which we had multiple individuals, populations of 27 formed monophyletic groups on our phylogenies, while 47 did not, indicating an urgent need for revisionary taxonomy at all levels of classification in this family.

Population genetic study of the U.S. federally listed Illinois cave amphipod, Gammarus acherondytes

Worldwide, conservation personnel must balance the needs of endangered species and humans. Studies that provide information of a species’ genetic structure can identify conservation units and help prioritize populations. We used a region of the cytochrome c oxidase subunit I gene to examine the population genetics of the U.S. federally listed Illinois cave amphipod, Gammarus acherondytes. Eleven unique haplotypes were identified from nine populations in two hydrologically separate subregions, each of which contained genetically distinct populations. This conclusion is based on (i) subregions form clades in the interspecific phylogeographic analyses; (ii) the between-subregions component in the Analysis of Molecular Variance accounted for a significant fraction (81.45%) of the genetic variation; and (iii) no haplotypes were shared between subregions. These results coincide with the known distribution of G. acherondytes and regional hydrology. We recommend future recovery efforts avoid mixing individuals between subregions to prevent the breakdown of local adaptive gene complexes.