David P. Mindell

Approaching a state shift in Earth’s biosphere

Localized ecological systems are known to shift abruptly and irreversibly from one state to another when they are forced across critical thresholds. Here we review evidence that the global ecosystem as a whole can react in the same way and is approaching a planetary-scale critical transition as a result of human influence. The plausibility of a planetary-scale ‘tipping point’ highlights the need to improve biological forecasting by detecting early warning signs of critical transitions on global as well as local scales, and by detecting feedbacks that promote such transitions. It is also necessary to address root causes of how humans are forcing biological changes.

Whole-genome analyses resolve early branches in the tree of life of modern birds

To better determine the history of modern birds, we performed a genome-scale phylogenetic analysis of 48 species representing all orders of Neoaves using phylogenomic methods created to handle genome-scale data. We recovered a highly resolved tree that confirms previously controversial sister or close relationships. We identified the first divergence in Neoaves, two groups we named Passerea and Columbea, representing independent lineages of diverse and convergently evolved land and water bird species. Among Passerea, we infer the common ancestor of core landbirds to have been an apex predator and confirm independent gains of vocal learning. Among Columbea, we identify pigeons and flamingoes as belonging to sister clades. Even with whole genomes, some of the earliest branches in Neoaves proved challenging to resolve, which was best explained by massive protein-coding sequence convergence and high levels of incomplete lineage sorting that occurred during a rapid radiation after the Cretaceous-Paleogene mass extinction event about 66 million years ago.

Comparative genomics reveals insights into avian genome evolution and adaptation

Birds are the most species-rich class of tetrapod vertebrates and have wide relevance across many research fields. We explored bird macroevolution using full genomes from 48 avian species representing all major extant clades. The avian genome is principally characterized by its constrained size, which predominantly arose because of lineage-specific erosion of repetitive elements, large segmental deletions, and gene loss. Avian genomes furthermore show a remarkably high degree of evolutionary stasis at the levels of nucleotide sequence, gene synteny, and chromosomal structure. Despite this pattern of conservation, we detected many non-neutral evolutionary changes in protein-coding genes and noncoding regions. These analyses reveal that pan-avian genomic diversity covaries with adaptations to different lifestyles and convergent evolution of traits.

Interordinal Relationships of Birds and Other Reptiles Based on Whole Mitochondrial Genomes

Several different groups of birds have been proposed as being the oldest or earliest diverging extant lineage within the avian phylogenetic tree, particularly ratites (Struthioniformes), waterfowl (Anseriformes), and shorebirds (Charadriiformes). Difficulty in resolving this issue stems from several factors, including the relatively rapid radiation of primary (ordinal) bird lineages and the lack of characters from an extant outgroup for birds that is closely related to them by measure of time. To help resolve this question, we have sequenced entire mitochondrial genomes for five birds (a rhea, a duck, a falcon, and two perching birds), one crocodilian, and one turtle. Maximum parsimony and maximum likelihood analyses of these new sequences together with published sequences (18 taxa total) yield the same optimal tree topology, in which a perching bird (Passeriformes) is sister to all the other bird taxa. A basal position for waterfowl among the bird study taxa is rejected by maximum likelihood analyses. However, neither the conventional view, in which ratites (including rhea) are basal to other birds, nor tree topologies with falcon or chicken basal among birds could be rejected in the same manner. In likelihood analyses of a subset of seven birds, alligator, and turtle (9 taxa total), we find that increasing the number of parameters in the model shifts the optimal topology from one with a perching bird basal among birds to the conventional view with ratites diverging basally; moreover, likelihood scores for the two trees are not significantly different. Thus, although our largest set of taxa and characters supports a tree with perching birds diverging basally among birds, the position of this earliest divergence among birds appears unstable. Our analyses indicate a sister relationship between a waterfowl/chicken clade and ratites, relative to perching birds and falcon. We find support for a sister relationship between turtles and a bird/crocodilian clade, and for rejecting both the Haemothermia hypothesis (birds and mammals as sister taxa) and the placement of turtles as basal within the phylogenetic tree for amniote animals.

rtREV: An amino acid substitution matrix for inference of retrovirus and reverse transcriptase phylogeny

Retroviral and other reverse transcriptase (RT)-containing sequences may be subject to unique evolutionary pressures, and models of molecular sequence evolution developed using other kinds of sequences may not be optimal. Here we develop and present a new substitution matrix for maximum likelihood (ML) phylogenetic analysis which has been optimized on a dataset of 33 amino acid sequences from the retroviral Pol proteins. When compared to other matrices, this model (rtREV) yields higher log-likelihood values on a range of datasets including lentiviruses, spumaviruses, betaretroviruses, gammaretroviruses, and other elements containing reverse transcriptase. We provide evidence that rtREV is a more realistic evolutionary model for analyses of the pol gene, although it is inapplicable to analyses involving the gag gene.

CHAPTER 8 – Phylogenetic Relationships among and within Select Avian Orders Based on Mitochondrial DNA

Among the many challenges facing avian systematists is the need for additional discrete character data sets and knowledge of the constraints influencing the character change over time. The objective of this chapter is to present phylogenetic analyses of new molecular sequence data for select avian lineages, to place these analyses in the context of existing phylogenetic hypotheses, and to discuss pertinent issues regarding methods of phylogenetic inference. Phylogenetic analyses presented in this chapter, based on mitochondrial DNA characters, address a number of controversial issues. Anseriformes and Galliformes are supported as sister taxa that are more closely related to a paleognath ( Rhea ) than to a set of neognaths. Placement of the root is critical in this latter determination, and addition of sequences from more taxa within the avian ingroup and within the crocodilian outgroup clade (including alligatorids, crocodilids, and gavialids) may help reduce the potential attraction among long branches. It is doubtful, however, that greater sampling of extant forms will ever eliminate the problem entirely. In analyses of two different data sets, Passeriformes are indicated as basal among five lineages representing the oldest divergences among extant birds and among a set of neognaths.

Molecular systematics of primary reptilian lineages and the tuatara mitochondrial genome.

We provide phylogenetic analyses for primary Reptilia lineages including, for the first time, Sphenodon punctatus (tuatara) using data from whole mitochondrial genomes. Our analyses firmly support a sister relationship between Sphenodon and Squamata, which includes lizards and snakes. Using Sphenodon as an outgroup for select squamates, we found evidence indicating a sister relationship, among our study taxa, between Serpentes (represented by Dinodon) and Varanidae. Our analyses support monophyly of Archosauria, and a sister relationship between turtles and archosaurs. This latter relationship is congruent with a growing set of morphological and molecular analyses placing turtles within crown Diapsida and recognizing them as secondarily anapsid (lacking a skull fenestration). Inclusion of Sphenodon, as the only surviving member of Sphenodontia (with fossils from the mid-Triassic), helps to fill a sampling gap within previous analyses of reptilian phylogeny. We also report a unique configuration for the mitochondrial genome of Sphenodon, including two tRNA(Lys) copies and an absence of ND5, tRNA(His), and tRNA(Thr) genes.

Molecular evidence of HIV-1 transmission in a criminal case

A gastroenterologist was convicted of attempted second-degree murder by injecting his former girlfriend with blood or blood-products obtained from an HIV type 1 (HIV-1)-infected patient under his care. Phylogenetic analyses of HIV-1 sequences were admitted and used as evidence in this case, representing the first use of phylogenetic analyses in a criminal court case in the United States. Phylogenetic analyses of HIV-1 reverse transcriptase and env DNA sequences isolated from the victim, the patient, and a local population sample of HIV-1-positive individuals showed the victims HIV-1 sequences to be most closely related to and nested within a lineage comprised of the patients HIV-1 sequences. This finding of paraphyly for the patients sequences was consistent with the direction of transmission from the patient to the victim. Analysis of the victims viral reverse transcriptase sequences revealed genotypes consistent with known mutations that confer resistance to AZT, similar to those genotypes found in the patient. A priori establishment of the patient and victim as a suspected transmission pair provided a clear hypothesis for phylogenetic testing. All phylogenetic models and both genes examined strongly supported the close relationship between the HIV-1 sequences of the patient and the victim. Resampling of blood from the suspected transmission pair and independent sequencing by different laboratories provided precaution against laboratory error.

Phylogeny of Tetraoninae and other galliform birds using mitochondrial 12S and ND2 genes

The avian subfamily Tetraoninae (grouse and ptarmigan) is a Holarctic group in the order Galliformes distinguished by morphological adaptations to cold environments and behavioral traits associated with elaborate courtship. Here we investigate the relationships of 17 tetraonines and 12 other galliform species using mitochondrial 12S and ND2 sequence data. We found support for the recent phylogenetic classification that separates the genus Dendragapus into two genera, Falcipennis and Dendragapus. In addition, we found support for a tetraonine clade in which the first divergence is between Bonasa umbellus and all others, followed by divergence between a Bonasa bonasia/Bonasa sewerzowi clade and the remaining tetraonines. Falcipennis canadensis is sister to a clade with four Tetrao species, and the genus Centrocercus is sister to a Dendragapus obscurus/Tympanuchus clade. Our data indicate a basal position for Cracidae and Megapodiidae among the five recognized galliform families. We also found strong support for the monophyly of Phasianidae, although the relative positions of Numididae and Odontiphoridae remains unresolved. We use a maximum likelihood approach to infer ages of 37mya for divergence of Numididae and Phasianidae and 28mya for the divergence of Tetraoninae and Meleagris gallopavo. These estimates must be viewed as tentative as they depend on tests of rates of molecular evolution and accurate fossil dates.

Assessing the Cretaceous Superordinal Divergence Times within Birds and Placental Mammals by Using Whole Mitochondrial Protein Sequences and an Extended Statistical Framework

Using the set of all vertebrate mtDNA protein sequences published as of May 1998, plus unpublished examples for elephant and birds, we examined divergence times in Placentalia and Aves. Using a parsimony-based test, we identified a subset of slower evolutionary rate placental sequences that do not appear to violate the clock assumption. Analyzing just these sequences decreases support for Marsupionta and the carnivore + perissodactyl group but increases support for armadillo diverging earlier than rabbit (which may represent the whole Glires group). A major theme of the paper is to use more comprehensive estimates of divergence time standard error (SE). From the well-studied horse/rhino split, estimated to be 55 million years before present (mybp), the splitting time within carnivores is confidently shown to be older than 50 million years. Some of our estimates of divergence times within placentals are relatively old, at up to 169 million years, but are within 2 SE of other published estimates. The whale/cow split at 65 mybp may be older than commonly assumed. All the sampled splits between the main groups of fereuungulates (the clade of carnivores, cetartiodactyls, perissodactyls, and pholidotes) seem to be distinctly before the Cretaceous/Tertiary boundary. Analyses suggest a close relationship between elephants (representing Afrotheria) and armadillos (Xenarthra), and our timing of this splitting is coincident with the opening of the South Atlantic, a major vicariant event. Recalibrating with this event (at 100 mybp), we obtain younger estimates for the earliest splits among placentals. Divergence times within birds are also assessed by using previously unpublished sequences. We fail to reject a clock for all bird taxa available. Unfortunately, available deep calibration points for birds are questionable, so a new calibration based on the age of the Anseriform stem lineage is estimated. The divergence time of rhea and ostrich may be much more recent than commonly assumed, while that of passerines may be older. Our major concern is the rooting point of the bird subtree, as the nearest outgroup (alligator) is very distant.