'Molecules and monkeys': George Gaylord Simpson and the challenge of molecular evolution

In this paper, I analyze George Gaylord Simpson's response to the molecularization of evolutionary biology from his unique perspective as a paleontologist. I do so by exploring his views on early attempts to reconstruct phylogenetic relationships among primates using molecular data. Particular attention is paid to Simpson's role in the evolutionary synthesis of the 1930s and 1940s, as well as his concerns about the rise of molecular biology as a powerful discipline and world-view in the 1960s. I argue that Simpson's belief in the supremacy of natural selection as the primary driving force of evolution, as well as his view that biology was a historical science that seeks ultimate causes and highlights contingency, prevented him from acknowledging that the study of molecular evolution was an inherently valuable part of the life sciences.     

Species and paleoanthropology

The biotic world is self-evidently “packaged” into units, of which the most basic is the species. It is necessary to develop an accurate understanding of what species are and how they are to be identified before we can proceed to more complex analyses of the evolutionary histories and relationships of extinct and extant taxa at all levels of the systematic hierarchy. In this article, we review the major species concepts current today among paleoanthropologists, and examine the limitations of their applicability to practical studies of extant and extinct faunas. The primary such limitation for paleoanthropologists is the fact that all major species definitions stress reproductive continuity (whether by exclusionary or inclusionary mechanisms), a quality that is inferential at best among forms known only as fossils (and, in many cases, in the extant fauna as well). The only reliable signal as to species status in the fossil record is morphology, yet speciation carries with it no specifiable quantity of morphological innovation. Some groups with autapomorphies are not species, and some species do not bear autapomorphies. How, then, are we to recognize species in the hominid and other fossil records? Noting that osteodental differences among congeneric primate species tend to be subtle, and that when consistent identifiable “morphs” can be found at least as many species are present, we recommend equating morphs based on several characters with species—realizing that only one or two distinctive characters may not make a morph. In this way, our views of the phylogenetic histories of higher taxa may be oversimplified, but their essential patterns will not be distorted.     

The problems of the Pliopithecidae as a hylobatid ancestor

Various members of the Pliopithecidae (Pliopithecus, Laccopithecus) and the Proconsulidae (Micropithecus, Dendropithecus, Limnoputhecus, Dionysopithecus, and Platdontopithecus) have been proposed as the ancestral hylobatid (gibbon), based largely on small size and simple-cusped, ape-like molars. However, this ignores evidence presented in early anatomical studies of living brachiating primates. All apes and several South American monkeys show structural anatomical adaptations for brachiation. The Pliopithecidae show some ceboid-like features in the hindlimb which suggest that this genus may have been partly suspensory and possibly comparable to spider monkeys, but without a prehensile tail. They were basically arboreal quadrupedal monkeys without any of the brachiator specializations. Large bodied apes add more traits in order to handle great weight. Among the small-bodied brachiators, only the hylobatids possess these large-brachiator traits. Such modifications serve no purpose other than to support a weight greater than 30 kg. The hylobatid gestation time and longevity are also characteristic only of much larger animals. The ancestral gibbon must have been among the large-bodied sivapithecines. This relationship is supported by body size, geography, and biochemical timing (pliopithecids were probably a distinct lineage in the late Oligocene). If a memeber of the Pliopithecidae were the ancestor of extant hylobatids, it would have had to have grown large, became adapted to brachiation, and then grown small again.Laccopithecus has been newly proposed as the ancestral gibbon. If it is not a member of the pliopithecids, with an age of less than 8 mya, then it could be a fossil hylobatid. It would have had to have separated from the Asian great ape line approximately 15 mya, developed full brachiation, and undergone a reduction in body size and dental sexual dimorphism.     

Hominoid cytogenetics and evolution

Much of the literature on the chromosomes of the Hominoidea exists in virtual isolation from both evolutionary theory and physical anthropology. Several unjustified speculations about hominoid affinities in the literature of cytogenetics may be attributed to the effects of this isolation. In this paper, the literature of comparative hominoid cytogenetics is reviewed, and that on chromosomal band patterns and repetitive DNA distributions relative to current evolutionary theory is discussed. These data are critically analyzed and shown to be more consistent with an orthodox hominoid phylogeny than with heterodox phylogenies. Rates and modes of karyotypic evolution are also discussed in an attempt to begin to assimilate the study of hominoid chromosomes within the framework of physical anthropology.     

Phylogeny and Evolution in Cariceae (Cyperaceae): Current Knowledge and Future Directions

The goal of this study was to review the impact of DNA sequence analyses on our understanding of Cariceae phylogeny, classification and evolution. To explore character evolution, 105 taxa from four different studies were included in an nrDNA ITS + ETS 1f analysis of all recognized genera (Carex, Cymophyllus, Kobresia, Schoenoxiphium, Uncinia) and Carex subgenera (Carex, Psyllophora, Vignea, Vigneastra). As in previous analyses, four major Cariceae clades were recovered: (1) a “Core Carex Clade” (subg. Carex, Vigneastra, Psyllophora p.p); (2) A “Vignea Clade” (subg. Vignea, Psyllophora p.p.); (3) a “Schoenoxiphium Clade” (Schoenoxiphium, subg. Psyllophora p.p.), and (4) a “Core Unispicate Clade” (Uncinia, Kobresia, subg. Psyllophora p.p.). All studies provide strong support (86–100% BS) for the Core Carex and Vignea Clades, but only weak to moderate support (<50%–78% BS) for the Core Unispicate and Schoenoxiphium Clades. The relationships of these groups are unresolved. Studies suggest that Carex is either paraphyletic with respect to all Cariceae genera or to all genera except Schoenoxiphium. Kobresia is a grade, but Uncinia and possibly Schoenoxiphium are monophyletic. The monotypic Cymophyllus is indistinct from Carex subg. Psyllophora species. Character analyses indicate that inflorescence proliferation and reduction have occurred in all major clades, and that the Cariceae’s unisexual flowers have evolved from perfect flowers. The ancestor to Cariceae possessed a multispicate inflorescence with cladoprophylls and female spikelets with tristigmatic gynoecia and closed utricles. This morphology is most similar to extant Carex subg. Carex species, which contradicts the nearly unanimous assumption that the highly compound inflorescences of Schoenoxiphium are primitive. Since taxonomic sampling and statistical support for phylogenies have generally been poor, we advocate the temporary maintenance of the four traditional Carex subgenera with androgynous unispicate species placed within subg. Psyllophora and dioecious and gynaecandrous unispicate species distributed amongst subgenera Carex and Vignea. A collective effort focused on developing new nuclear markers, on increasing taxonomic and geographic sampling, and on studying development within the context of phylogeny, is needed to develop a phylogenetic classification of Cariceae.     

Hominoid heterochromatin: Terminal C-bands as a complex genetic trait linking chimpanzee and gorilla

The genetic relations of the apes have been the source of contention throughout the last decade. A potentially useful suite of phylogenetic characters is the distribution of darkly staining material (heterochromatin) in the chromosomes of the apes. While the precise etiology of this character suite remains unclear, it appears to be fairly easily reconciled to hominoid phylogeny in general. The distribution of heterochromatin at the tips of the chromosomes of gorillas and chimpanzees suggests a phylogenetic association between those two taxa exclusive of humans. © 1993 Wiley-Liss, Inc.     

Blood will tell (won't it?): A century of molecular discourse in anthropological systematics

Being derived from the hereditary material, molecular genetic data are often assumed to be a source of sounder inferences about evolution than data from other kinds of investigations. This, however, tends to be taken in the absence of a clear knowledge of the evolutionary processes at work, the technical shortcomings, and the manner of deriving the specific conclusions. The history of biological anthropology shows that, from the beginning of the 20th century, grossly naive conclusions have been promoted simply on the basis that they are derived from genetics, without having been fully thought-out. A balanced consideration of the shortcomings as well as the advantages of genetic data are necessary for its proper integration into the field. When molecular and morphological data disagree, both must be reexamined carefully, for genetics has been used irresponsibly as a form of scientific validation, both in American society and in American science. Contemporary data bearing on the molecular relationships of the apes are noteworthy for their diversity in quality, and need to be evaluated in the light of molecular and microevolutionary theory. © 1994 Wiley-Liss, Inc.     

Relationships among rodent taxa as indicated by reproductive biology1

Demonstrated that in rodents the duration of ontogenetic development (from conception to the age of eye openin) is allometrically related to the maternal body weight. The differences between actual developmental time and the expected time (counted for animals of that systematic position and that body weight) can be used as a tool to test phylogenetic relationships. As far as the relationships between sister-taxa are concerned, the results of the present analysis corroborate the conclusions of modern classifications. A long developmental time (which means by implication also a long pregnancy and precocity) is couled with hystricognathy and hystricomorhy. These traits must be considered plesiomorphic and their occurrence suggests conservatism of articular taxa. Parallell (coupled) with adopting sciurognathy and, particularly, protrogomorpiy, sciuromorphy, and eventually, myomorphy, rodents were able to shorten their developmental times. In this way they could increase the reproductive rate and made their reproduction more efficient. Consequently the respective taxa radiated more rapidly and successfully.     

Incisor-molar relationships in chimpanzees and other hominoids: implications for diet and phylogeny

In chimpanzees, the cutting edge of the incisor battery is longer in relation to the length of the molar row than in any other hominoid, extant or fossil, the only other lineage approaching it being the orangutan. Apart from their increased mesio-distal dimensions, the upper and lower incisors of chimpanzees differ in additional ways from those of almost all other hominoids. The I2/ is enlarged, so that the difference in size between it and the central upper incisor is less than it is in the heteromorphic upper incisors of other hominoids. The lower incisors are expanded mesio-distally, so much so that isolated I/2 crowns can resemble upper central incisors. In chimpanzees the lingual surface of the lower incisors is generally more procumbent than it is in other hominoids, which have more vertically oriented incisor crowns and there is a greater difference in enamel thickness between labial and lingual sides. The re-orientation of the lower incisor crown is reflected in the root, which in lateral view is anteriorly concave in chimpanzees whereas it is more orthogonal or convex in other hominoids. The molars of chimpanzees, especially the lowers, have extensive and relatively deep occlusal basins, and the main cusps are peripheralised and labio-lingually compressed, making them more trenchant than those of other hominoids. This paper examines the incisor-lower molar proportions in extinct and living hominoids and develops a new hypothesis about the evolution of the dentition of chimpanzees and links it to their diet. It also examines the incisor-molar proportions of hominids and African apes in order to throw light on the phylogenetic relationships between them. It is shown that chimpanzees are highly derived in this respect and that several recent ideas concerning the chimp-like appearance of the last common ancestor of hominids and African apes are likely to be incorrect.This revised version was published online in April 2005 with corrections to the cover date of the issue.     

变豆菜属分类、起源与进化研究进展

变豆菜属(Sanicula)是典型的东亚-北美间断分布属,属于北极-第三纪古老区系成分。目前全世界有40种,中国(17种,11个特有种)和美国(22种,13个特有种)是2个分布中心。近年来有关变豆菜属分子系统发育研究表明该属并非单系,不同学者采用了不同的属下分类标准,但属下分类系统和种间界限仍存在争议,特别是药用植物的种类较易混淆。变豆菜属的系统进化研究主要集中在北美Sanicora DC.组及夏威夷Sandwicensis Shan and Constance组的类群,缺少对中国特有种的研究,因此该属的系统位置、起源地、迁移、扩散模式和种间进化关系均不清楚。本文对变豆菜属的分类系统、分类方法、起源和进化的研究进展进行了综述,并提出存在的问题和解决方法。     

Genomic analysis and expression investigation of caleosin gene family in Arabidopsis

Caleosin is a common lipid-droplet surface protein, which has the ability to bind calcium. Arabidopsis (Arabidopsis thaliana) is considered a model organism in plant researches. Although there are growing researches about caleosin in the past few years, a systemic analysis of caleosins in Arabidopsis is still scarce. In this study, a comprehensive investigation of caleosins in Arabidopsis was performed by bioinformatics methods. Firstly, eight caleosins in Arabidopsis are divided into two types, L-caleosin and H-caleosin, according to their molecular weights, and these two types of caleosin have many differences in characteristics. Secondly, phylogenetic tree result indicates that L-caleosin may evolve from H-caleosin. Thirdly, duplication pattern analysis shows that segmental and tandem duplication are main reasons for Arabidopsis caleosin expansion with the equal part. Fourthly, the expression profiles of caleosins are also investigated in silico in different organs and under various stresses and hormones. In addition, based on promoter analysis, caleosin may be involved in calcium signal transduction and lipid accumulation. Thus, the classification and expression analysis of caleosin genes in Arabidopsis provide facilities to the research of phylogeny and functions in this gene family.     

Human uniqueness and theoretical content in paleoanthropology

One of the things that distinguishes science from nonscientific discourse is the incorporation of its hypotheses into theoretical structures. Like parapsychology, the study of human evolution lacks theoretical content and connections. This lack is due, in part, to the collapse of the classical primatological synthesis in the 1970s. It is due in larger measure to a persistent anthropological focus on human uniqueness as the phenomenon to be explained. Such supposedly unique human features as large brains, language, conceptual thinking, and upright bipedalism are uniquely human by definition rather than as a matter of empirical fact. Much scientific effort and ingenuity has gone into redefining such characteristics whenever discoveries about other animals have posed a threat to human uniqueness. But since by definition qualitatively unique phenomena do not conform to overarching laws that apply to similar cases, they must remain theoretically inexplicable. Paleoanthropology should aim at increasing its theoretical content by reducing the list of qualitative human uniquenesses-and eliminating it altogether if possible.If man wants to set up a contest in resembling himself and award himself the prize, no one will quarrel with him.     

植物几丁质酶的结构与功能、分类及进化

近年来对几丁质酶的研究越来越深入,资料也愈来愈多,有的植物几丁质酶除具有几丁质酶活性,还具有其它的活性,典型的几丁质酶由－N－端信号区,催化区和C－端延伸区组成,有的还有几丁质结合域,各项能域具有各自的功能,对植物几丁质酶的分类已经过多次改进,目前公认的分成4组9个亚组,有证据表明植物几丁质酶在进化过程中有遗传转座现象,但具有进化过程还有待进一步确证,对几丁质酶与其它一些蛋白的关系的了解有助于理解几丁质酶的起源和进化,由于几丁质酶具有独特的抗真菌特性,因而几丁质酶基因成为目前抗真菌基因工程研究的热之一。     

A Photometric Method for Determining the Growth Rate of Yeast (Saccharomyces cereviciae)

There have been several investigations into students' conceptions of animal classification. Previous research has generally failed to study the criteria of classification used by the students. This study shows that students prefer to classify creatures along the criteria of habitat and locomotion (method of movement). They continue using these criteria even after learning the categories of biological taxonomy. The results lead to the assumption of an implicit theory of natural kinship of animals. The educational consequences for biology instruction, especially with regard to biological taxonomy, biodiversity, and evolution, are discussed.     

The relative congruence of cranial and genetic estimates of hominoid taxon relationships: implications for the reconstruction of hominin phylogeny

Previous analyses of extant catarrhine craniodental morphology have often failed to recover their molecular relationships, casting doubt on the accuracy of hominin phylogenies based on anatomical data. However, on the basis of genetic, morphometric and environmental affinity patterns, a growing body of literature has demonstrated that particular aspects of cranial morphology are remarkably reliable proxies for neutral modern human population history. Hence, it is important to test whether these intra-specific patterns can be extrapolated to a broader primate taxon level such that inference rules for understanding the morphological evolution of the extinct hominins may be devised. Here, we use a matrix of molecular distances between 15 hominoid taxa to test the genetic congruence of 14 craniomandibular regions, defined and morphometrically delineated on the basis of previous modern human analyses. This methodology allowed us to test directly whether the cranial regions found to be reliable indicators of population history were also more reliable proxies for hominoid genetic relationships. Cranial regions were defined on the basis of three criteria: developmental-functional units, individual bones, and regions differentially affected by masticatory stress. The results found that all regions tested were significantly and strongly correlated with the molecular matrix. However, the modern human predictions regarding the relative congruence of particular regions did not hold true, as the face was statistically the most reliable indicator of hominoid genetic distances, as opposed to the vault or basicranium. Moreover, when modern humans were removed from the analysis, all cranial regions improved in their genetic congruence, suggesting that it is the inclusion of morphologically-derived humans that has the largest effect on incongruence between morphological and molecular estimates of hominoid relationships. Therefore, it may be necessary to focus on smaller intra-generic taxonomic levels to more fully understand the effects of neutral and selective evolutionary processes in generating morphological diversity patterns.