A reassessment of mammalian alpha A-crystallin sequences using DNA sequencing: implications for anthropoid affinities of tarsier

Primate phylogenomics uncovers multiple rapid radiations and ancient interspecific introgression

Our understanding of the evolutionary history of primates is undergoing continual revision due to ongoing genome sequencing efforts. Bolstered by growing fossil evidence, these data have led to increased acceptance of once controversial hypotheses regarding phylogenetic relationships, hybridization and introgression, and the biogeographical history of primate groups. Among these findings is a pattern of recent introgression between species within all major primate groups examined to date, though little is known about introgression deeper in time. To address this and other phylogenetic questions, here, we present new reference genome assemblies for 3 Old World monkey (OWM) species: Colobus angolensis ssp. palliatus (the black and white colobus), Macaca nemestrina (southern pig-tailed macaque), and Mandrillus leucophaeus (the drill). We combine these data with 23 additional primate genomes to estimate both the species tree and individual gene trees using thousands of loci. While our species tree is largely consistent with previous phylogenetic hypotheses, the gene trees reveal high levels of genealogical discordance associated with multiple primate radiations. We use strongly asymmetric patterns of gene tree discordance around specific branches to identify multiple instances of introgression between ancestral primate lineages. In addition, we exploit recent fossil evidence to perform fossil-calibrated molecular dating analyses across the tree. Taken together, our genome-wide data help to resolve multiple contentious sets of relationships among primates, while also providing insight into the biological processes and technical artifacts that led to the disagreements in the first place.

Combining three newly sequenced primate genomes with other published genomes, this study adapts a little-known method for detecting ancient introgression to genome-scale data, revealing multiple previously unknown examples of hybridization between primate species.

Estimating the phylogeny and divergence times of primates using a supermatrix approach

Background

The primates are among the most broadly studied mammalian orders, with the published literature containing extensive analyses of their behavior, physiology, genetics and ecology. The importance of this group in medical and biological research is well appreciated, and explains the numerous molecular phylogenies that have been proposed for most primate families and genera. Composite estimates for the entire order have been infrequently attempted, with the last phylogenetic reconstruction spanning the full range of primate evolutionary relationships having been conducted over a decade ago.

Results

To estimate the structure and tempo of primate evolutionary history, we employed Bayesian phylogenetic methods to analyze data supermatrices comprising 7 mitochondrial genes (6,138 nucleotides) from 219 species across 67 genera and 3 nuclear genes (2,157 nucleotides) from 26 genera. Many taxa were only partially represented, with an average of 3.95 and 5.43 mitochondrial genes per species and per genus, respectively, and 2.23 nuclear genes per genus. Our analyses of mitochondrial DNA place Tarsiiformes as the sister group of Strepsirrhini. Within Haplorrhini, we find support for the primary divergence of Pitheciidae in Platyrrhini, and our results suggest a sister grouping of African and non-African colobines within Colobinae and of Cercopithecini and Papionini within Cercopthecinae. Date estimates for nodes within each family and genus are presented, with estimates for key splits including: Strepsirrhini-Haplorrhini 64 million years ago (MYA), Lemuriformes-Lorisiformes 52 MYA, Platyrrhini-Catarrhini 43 MYA and Cercopithecoidea-Hominoidea 29 MYA.

Conclusion

We present an up-to-date, comprehensive estimate of the structure and tempo of primate evolutionary history. Although considerable gaps remain in our knowledge of the primate phylogeny, increased data sampling, particularly from nuclear loci, will be able to provide further resolution.

SINE insertions in cladistic analyses and the phylogenetic affiliations of Tarsius bancanus to other primates

Transpositions of Alu sequences, representing the most abundant primate short interspersed elements (SINE), were evaluated as molecular cladistic markers to analyze the phylogenetic affiliations among the primate infraorders. Altogether 118 human loci, containing intronic Alu elements, were PCR analyzed for the presence of Alu sequences at orthologous sites in each of two strepsirhine, New World and Old World monkey species, Tarsius bancanus, and a nonprimate outgroup. Fourteen size-polymorphic amplification patterns exhibited longer fragments for the anthropoids (New World and Old World monkeys) and T. bancanus whereas shorter fragments were detected for the strepsirhines and the outgroup. From these, subsequent sequence analyses revealed three Alu transpositions, which can be regarded as shared derived molecular characters linking tarsiers and anthropoid primates. Concerning the other loci, scenarios are represented in which different SINE transpositions occurred independently in the same intron on the lineages leading both to the common ancestor of anthropoids and to T. bancanus, albeit at different nucleotide positions. Our results demonstrate the efficiency and possible pitfalls of SINE transpositions used as molecular cladistic markers in tracing back a divergence point in primate evolution over 40 million years old. The three Alu insertions characterized underpin the monophyly of haplorhine primates (Anthropoidea and Tarsioidea) from a novel perspective.

The effect of stress on the pattern of phosphorylation of alphaA and alphaB crystallin in the rat lens

Previously, we have shown that phosphorylation of alpha crystallin (alpha) in rat lenses can be stimulated by oxidative stress. To better understand the biological functions of the stress-induced phosphorylation of the A and B chains of alpha (alphaA and alphaB), the normal and stress-induced phosphorylation pattern of these polypeptides in the rat lens has been investigated. With either alphaA or alphaB, there is only one phosphorylation site that is significantly affected, with widely different stresses, H(2)O(2)or elevation in free Ca(++)levels. However, the phosphorylation sites are markedly different for the two polypeptides, for alphaA being on Thr-4 in the N terminal region and with alphaB on Ser-59 in the central region of the polypeptide. The difference in the sequence in the two phosphorylation regions suggests that different phosphorylation systems are probably involved. This implies that the cellular function of the phosphorylation of alphaA and alphaB may be quite different.

Nocturnal tarsier retina has both short and long/medium-wavelength cones in an unusual topography

The evolutionary position of tarsiers with respect to primates is still debated. The type of photoreceptors in the nocturnal Tarsius spectrum retina has been compared with the nocturnal New World monkey Aotus trivulgaris and the Old World monkey Macaca nemestrina by using immunocytochemical labeling for antisera known to be specific for primate cone and rod proteins. In all three species, antisera to long/medium (L/M) -wavelength specific cone opsin and cone-specific alpha-transducin detected a single row of cones. Only Macaca and tarsier retina contained cones labeled by antiserum to short (S) -wavelength specific cone opsin. Tarsier rod cell bodies were 6-12 deep, depending on retinal eccentricity. Tarsier central cones had 2-microm-wide outer (OS) and inner segments, which came straight off the cell body. Cone morphology differed little from rods except OS were shorter. Macaca cones labeled for 7G6 and calbindin, Aotus cones did not label for calbindin, and Tarsius cones did not label for 7G6 or calbindin. In tarsier retinal whole-mounts, peak cone density ranged from 11,600-14,200/cones mm(2). The 11- to 12-mm-wide peak region centered roughly on the optic disc, although foveal counts remain to be completed. Density decreased symmetrically to a far peripheral band of 4,200-7, 000/cones mm(2). In contrast, S cone density was very low in central retina (0-300/mm(2)), rose symmetrically with eccentricity, and peaked at 1,100-1,600/mm(2) in a 2- to 3-mm-wide zone in the far periphery. In this zone, S cones were 9-14% of all cones. L/M cones were regularly spaced, whereas S cones showed no regular distribution pattern. Although the functional characteristics of the tarsier S and L/M cone systems are yet to be determined, tarsier cone proteins and distribution have some similarities to both New and Old World monkey retinas.

Identification of sequence tagged sites in the Asian and African elephant

To date, gene identification in elephants has essentially related to evolutionary studies. Further identification of genes in elephants could provide additional information for evolutionary studies and for evaluating genetic diversity in existing elephant populations. The objective of this project was to identify sequence tagged sites (STSs) in the Asian and the African elephant for the following genes: melatonin receptor 1a (MTNR1A), retinoic acid receptor beta (RARB), and leptin receptor (LEPR). These genes are highly conserved among mammals, and all may play a role in reproduction. Heterologous primers for PCR were designed from sequences available in other species. Fragments of size 141 base pairs (bp) for RARB and 327 bp for LEPR were obtained by amplifying genomic Asian and African elephant DNA. The LEPR fragment included an intron of 164 bp. Also, a 417 bp fragment for MTNR1A was obtained in the Asian elephant only. All PCR products were sequenced and comparison computations were made at the nucleotide and amino acid levels to sequence available in the GenBank database. Nucleotide sequence for RARB was identical for both Asian and African elephants and differed by only 3 bp for LEPR. Deduced amino acid sequence was identical for both STSs in both species. Elephants were relatively similar in comparison to other mammals and less similar to chickens.