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PubMed1998

Spine injuries associated with falls from hunting tree stands.

Spinal injuries resulting from falls out of tree stands are often associated with concomitant neurologic deficit, prolonged hospitalization, and long-term disability. The purpose of this study was to review the types of spinal injuries that resulted from falls from hunting tree stands. We retrospectively reviewed 27 patients who came to our institution for treatment of spine injuries related to tree-stand accidents between 1981 and 1997. Eleven percent of the falls were alcohol related. Mean height of the fall was 19.6 feet (range, 10 to 35 feet). There were 17 burst fractures, 8 wedge compression fractures, 4 fractures involving the posterior elements, and 1 coronal fracture of the sacral body. Significant neurologic injury occurred in 12 patients (44%). Sixteen patients (59%) had associated injuries. Nine patients (33%) had open reduction, internal fixation, and fusion of their spine fractures. One patient was treated with a halo jacket. The remaining patients were treated in rigid, molded, polypropylene thoracolumbar orthoses or lumbosacral corsets. Accidental falls from tree stands may result in significant spinal fractures often associated with concomitant neurologic injury, extended hospitalization, and permanent disability. Many of these injuries may be prevented through aggressive hunter safety education.

Accidental Falls↗
PubMed1997

Structural trees for protein superfamilies.

Structural trees for large protein superfamilies, such as beta proteins with the aligned beta sheet packing, beta proteins with the orthogonal packing of alpha helices, two-layer and three-layer alpha/beta proteins, have been constructed. The structural motifs having unique overall folds and a unique handedness are taken as root structures of the trees. The larger protein structures of each superfamily are obtained by a stepwise addition of alpha helices and/or beta strands to the corresponding root motif, taking into account a restricted set of rules inferred from known principles of the protein structure. Among these rules, prohibition of crossing connections, attention to handedness and compactness, and a requirement for alpha helices to be packed in alpha-helical layers and beta strands in beta layers are the most important. Proteins and domains whose structures can be obtained by stepwise addition of alpha helices and/or beta strands to the same root motif can be grouped into one structural class or a superfamily. Proteins and domains found within branches of a structural tree can be grouped into subclasses or subfamilies. Levels of structural similarity between different proteins can easily be observed by visual inspection. Within one branch, protein structures having a higher position in the tree include the structures located lower. Proteins and domains of different branches have the structure located in the branching point as the common fold.

Animals↗
PubMed1997

Cardiac-like musculature of the intrapulmonary venous wall of the long-clawed shrew (Sorex unguiculatus), common tree shrew (Tupaia glis) and common marmoset (Callithrix jacchus).

BACKGROUND: The cardiac-like musculature is distributed not only in the heart wall but also in the intrapulmonary venous wall in a few species of insectivores. It has been suggested that the evolutionary origin of venous cardiac-like musculature may be traceable to a basic stock of certain mammalian lines of descent. So, it is important to clarify whether the musculature may be a common structure in lower mammals from insectivores to primates and to examine the functional significance of the structure. METHODS: The distribution of cardiac-like musculature in the intrapulmonary venous wall of the long-clawed shrew (Sorex unguiculatus), common tree shrew (Tupaia glis), and common marmoset (Callithrix jacchus) was observed by light and electron microscopy. The presence of atrial natriuretic polypeptide (ANP) was examined in the musculature by immunohistochemistry. RESULTS: All three species contained cardiac-like myocytes in the tunica media of intrapulmonary venous wall. In the common tree shrew and the common marmoset, cardiac-like musculature was found in the small intrapulmonary vein of 150-200 microns in diameter, while, in the long-clawed shrew, it was distributed even in the intrapulmonary vein of 30 microns in diameter. Ultrastructure of myocytes was fundamentally similar to that of atrial myocytes in the long-clawed shrew and the common tree shrew. The presence of atrial natriuretic polypeptide (ANP) was also demonstrated by immunohistochemistry in the intrapulmonary venous walls of common tree shrews. CONCLUSIONS: The results indicate that the pulmonary venous cardiac-like musculature occurs in the lower eutherian mammals from insectivores to primitive primates. The musculature is thought to act as a regulatory pump in pulmonary circulation and as an endocrine apparatus of ANP.

Animals↗
PubMed1996

Size-dependent morphology of the conductive bronchial tree in four species of myomorph rodents.

Size-dependent structural patterns in the conductive bronchial tree of four species of myomorph rodents of different body weight were determined by lung casts. The lungs of the harvest mouse, Micromys minutus, body weight 5-7 g, the house mouse, Mus musculus, body weight 35-45 g, the brown rat, Rattus norvegicus, body weight 200-400 g, and the African giant pouched rat, Cricetomys gambianus, body weight 1,200-1,800 g, were inflated to 20 cm H2O, frozen, freeze-dried, hardened, and filled with silicone rubber. The casts were pruned, and branching pattern, diameter, and volume of the conductive bronchial tree were determined using a binocular magnifier. All four species have four lobes on the right lung and an undivided left lung, and the central bronchial tree on either side shows an identical monopodial branching pattern. Although the ramification of the central conductive bronchi is not size-dependent, the diameter and volume are. The diameter of the left main bronchus equals 1.24% of body length in Micromys and 0.6% in Cricetomys, and the conductive bronchial tree makes up 13% of the total lung volume in Micromys and 6% in Cricetomys. Relatively wider airways and a decline in airway resistance with declining body mass in small mammals compared to large ones result in a high ventilatory dead space, which is compensated for by a higher breathing frequency.

Animals↗
PubMed2002

Classification trees as an alternative to linear discriminant analysis.

Linear discriminant analysis (LDA) is frequently used for classification/prediction problems in physical anthropology, but it is unusual to find examples where researchers consider the statistical limitations and assumptions required for this technique. In these instances, it is difficult to know whether the predictions are reliable. This paper considers a nonparametric alternative to predictive LDA: binary, recursive (or classification) trees. This approach has the advantage that data transformation is unnecessary, cases with missing predictor variables do not require special treatment, prediction success is not dependent on data meeting normality conditions or covariance homogeneity, and variable selection is intrinsic to the methodology. Here I compare the efficacy of classification trees with LDA, using typical morphometric data. With data from modern hominoids, the results show that both techniques perform nearly equally. With complete data sets, LDA may be a better choice, as is shown in this example, but with missing observations, classification trees perform outstandingly well, whereas commercial discriminant analysis programs do not predict classifications for cases with incompletely measured predictor variables and generally are not designed to address the problem of missing data. Testing of data prior to analysis is necessary, and classification trees are recommended either as a replacement for LDA or as a supplement whenever data do not meet relevant assumptions. It is highly recommended as an alternative to LDA whenever the data set contains important cases with missing predictor variables.

Animals↗
PubMed2003

Impact of character correlation and variable groupings on modern human population tree resolution.

Relationships among modern human populations are often explored through the use of linear measurements taken on the cranium and expressed in the form of dendrograms. However, craniometric variables are strongly correlated and thereby violate the assumption of independence that most statistical analyses require. This study explores the relationship between differing methods of variable treatment and the statistical robustness of the outcomes they yield, as depicted in interpopulational trees of relatedness among modern humans. Three methods of grouping variables are examined. The first method leaves them ungrouped, the second groups variables on the basis of the developmental and/or functional complex of the cranium to which they are thought to belong, and the last method reduces variables by using principal components analysis. The strength of each of these methods is tested through the use of the Continuous Character Maximum Likelihood (CONTML) program in the PHYLIP phylogeny inference package. This program produces output in the form of trees, and the resolution of the branching topology is given as a log-likelihood value, with statistical confidence intervals supporting each branch placement on the tree. The results indicate that leaving variables ungrouped provides misleadingly strong results by failing to account for character correlation. Of the alternative two grouping methods, the covarying components method yields the best-resolved tree with stronger statistical support for its topology than the approach of grouping variables on the basis of their location on the cranium. Finally, the implications for interpreting population histories based on such methods are discussed.

Adolescent↗
PubMed2003

The visual pulvinar in tree shrews II. Projections of four nuclei to areas of visual cortex.

Patterns of thalamocortical connections were related to architectonically defined subdivisions of the pulvinar complex and the dorsolateral geniculate nucleus (LGN) in tree shrews (Tupaia belangeri). Tree shrews are of special interest because they are considered close relatives of primates, and they have a highly developed visual system. Several distinguishable tracers were injected within and across cortical visual areas in individual tree shrews in order to reveal retinotopic patterns and cortical targets of subdivisions of the pulvinar. The results indicate that each of the three architectonic regions of the pulvinar has a distinctive pattern of cortical connections and that one of these divisions is further divided into two regions with different patterns of connections. Two of the pulvinar nuclei have similar retinotopic patterns of projections to caudal visual cortex. The large central nucleus of the pulvinar (Pc) projects to the first and second visual areas, V1 and V2, and an adjoining temporal dorsal area (TD) in retinotopic patterns indicating that the upper visual quadrant is represented dorsal to the lower quadrant in Pc. The smaller ventral nucleus (Pv) which stains darkly for the Cat-301 antigen, projects to these same cortical areas, with a retinotopic pattern. Pv also projects to a temporal anterior area, TA. The dorsal nucleus (Pd), which densely expresses AChE, projects to posterior and ventral areas of temporal extrastriate cortex, areas TP and TPI. A posterior nucleus, Pp, projects to anterior areas TAL and TI, of the temporal lobe, as well as TPI. Injections in different cortical areas as much as 6 mm apart labeled overlapping zones in Pp and double-labeled some cells. These results indicate that the visual pulvinar of tree shrews contains at least four functionally distinct subdivisions, or nuclei. In addition, the cortical injections revealed that the LGN projects topographically and densely to V1 and that a significant number of LGN neurons project to V2 and TD.

Acetylcholinesterase↗
PubMed2006

Organization of frontoparietal cortex in the tree shrew (Tupaia belangeri). I. Architecture, microelectrode maps, and corticospinal connections.

Despite extensive investigation of the motor cortex of primates, little is known about the organization of motor cortex in tree shrews, one of their closest living relatives. We investigated the organization of frontoparietal cortex in Belanger's tree shrews (Tupaia belangeri) by using intracortical microstimulation (ICMS), corticospinal tracing, and detailed histological analysis. The results provide evidence for the subdivision of tree shrew frontoparietal cortex into seven distinct areas (five are newly identified), including two motor fields (M1 and M2) and five somatosensory fields (3a, 3b, S2, PV, and SC). The types of movements evoked in M1 and M2 were similar, but M2 required higher currents to elicit movements and had few connections to the cervical spinal cord and distinctive cyto- and immunoarchitecture. The borders between M1 and the anterior somatosensory regions (3a and 3b) were identified primarily from histological analysis, because thresholds were similar between these regions, and differences in corticospinal neuron distribution were subtle. The caudal (SC) and lateral (S2 and PV) somatosensory fields were identified based on differences in architecture and distribution of corticospinal neurons. Myelin-dense modules were identified in lateral cortex, in the expected location of the oral, forelimb, and hindlimb representations of S2, and possibly PV. Evidence for a complex primate-like array of motor fields is lacking in tree shrews, but their motor cortex shares a number of basic features with that of primates, which are not found in more distantly related species, such as rats.

Animals↗
PubMed1991

Androgenic regulation of dendritic trees of motoneurons in the spinal nucleus of the bulbocavernosus: reconstruction after intracellular iontophoresis of horseradish peroxidase.

Androgen-sensitive motoneurons in the spinal nucleus of the bulbocavernosus (SNB) in adult male rats were labeled after intracellular iontophoresis of horseradish peroxidase, after which they were fully reconstructed in three dimensions in order to measure their dendritic trees. Three groups of rats were compared: intact adult male rats and male rats castrated as adults and given Silastic tube implants containing either testosterone or nothing. In the high-androgen groups (intact males and testosterone-treated castrates), soma size and the diameter of the first-order dendrites were larger than in blank-treated castrates. Moreover, the terminal dendrites in all groups possessed growth cones, implying that the dendrites of these motoneurons are capable of growth in adulthood. However, there were no statistically significant group differences in the length, membrane surface area, or volume of the dendritic trees, or in the orientation or branching symmetry of dendrites. In general, there were positive correlations between the size of the motoneuronal soma and various measures of the size of the dendritic tree and between the diameter of individual stem (first-order) dendritic branches and the size of remainder of that dendrite. These data suggest that there may be a modest effect of androgen on the size of the dendritic trees of SNB motoneurons in adulthood, although the effect is much smaller than has previously been reported.

Androgens↗
PubMed2005

Synaptic integration in dendritic trees.

Most neurons have elaborate dendritic trees that receive tens of thousands of synaptic inputs. Because postsynaptic responses to individual synaptic events are usually small and transient, the integration of many synaptic responses is needed to depolarize most neurons to action potential threshold. Over the past decade, advances in electrical and optical recording techniques have led to new insights into how synaptic responses propagate and interact within dendritic trees. In addition to their passive electrical and morphological properties, dendrites express active conductances that shape individual synaptic responses and influence synaptic integration locally within dendrites. Dendritic voltage-gated Na(+) and Ca(2+) channels support action potential backpropagation into the dendritic tree and local initiation of dendritic spikes, whereas K(+) conductances act to dampen dendritic excitability. While all dendrites investigated to date express active conductances, different neuronal types show specific patterns of dendritic channel expression leading to cell-specific differences in the way synaptic responses are integrated within dendritic trees. This review explores the way active and passive dendritic properties shape synaptic responses in the dendrites of central neurons, and emphasizes their role in synaptic integration.

Action Potentials↗
PubMed2007

Routes are trees: the parsing perspective on protein folding.

An important puzzle in structural biology is the question of how proteins are able to fold so quickly into their unique native structures. There is much evidence that protein folding is hierarchic. In that case, folding routes are not linear, but have a tree structure. Trees are commonly used to represent the grammatical structure of natural language sentences, and chart parsing algorithms efficiently search the space of all possible trees for a given input string. Here we show that one such method, the CKY algorithm, can be useful both for providing novel insight into the physical protein folding process, and for computational protein structure prediction. As proof of concept, we apply this algorithm to the HP lattice model of proteins. Our algorithm identifies all direct folding route trees to the native state and allows us to construct a simple model of the folding process. Despite its simplicity, our model provides an account for the fact that folding rates depend only on the topology of the native state but not on sequence composition.

Algorithms↗
PubMed2007

A comparison of regression trees, logistic regression, generalized additive models, and multivariate adaptive regression splines for predicting AMI mortality.

Clinicians and health service researchers are frequently interested in predicting patient-specific probabilities of adverse events (e.g. death, disease recurrence, post-operative complications, hospital readmission). There is an increasing interest in the use of classification and regression trees (CART) for predicting outcomes in clinical studies. We compared the predictive accuracy of logistic regression with that of regression trees for predicting mortality after hospitalization with an acute myocardial infarction (AMI). We also examined the predictive ability of two other types of data-driven models: generalized additive models (GAMs) and multivariate adaptive regression splines (MARS). We used data on 9484 patients admitted to hospital with an AMI in Ontario. We used repeated split-sample validation: the data were randomly divided into derivation and validation samples. Predictive models were estimated using the derivation sample and the predictive accuracy of the resultant model was assessed using the area under the receiver operating characteristic (ROC) curve in the validation sample. This process was repeated 1000 times-the initial data set was randomly divided into derivation and validation samples 1000 times, and the predictive accuracy of each method was assessed each time. The mean ROC curve area for the regression tree models in the 1000 derivation samples was 0.762, while the mean ROC curve area of a simple logistic regression model was 0.845. The mean ROC curve areas for the other methods ranged from a low of 0.831 to a high of 0.851. Our study shows that regression trees do not perform as well as logistic regression for predicting mortality following AMI. However, the logistic regression model had performance comparable to that of more flexible, data-driven models such as GAMs and MARS.

Data Interpretation, Statistical↗
PubMed1994

Prevention of collagen crosslinking increases form-deprivation myopia in tree shrew.

To examine whether collagen crosslinking is important for the regulation of refractive development, tree shrews were treated with agents that block collagen crosslinking [beta-aminoproprionitrile (beta-APN), or D-penicillamine (DPA)] and underwent monocular deprivation (MD) of form vision by eyelid closure to induce myopia. MD began on the first day of visual exposure and continued for 75 days. After 15-20 days of visual exposure, daily intraperitoneal injections of beta-APN (beta-APN MD animals, n = 5) or DPA (DPA MD animals, n = 5) were administered for 17-21 days. beta-APN open animals (n = 5) received the same injection schedule, but both eyes remained open. Saline MD animals (n = 5) received i.p. saline and MD. At 75 days of visual exposure, the MD eyes of beta-APN treated tree shrews were highly myopic (-23.6 +/- 3.3 D) in comparison to their open control eyes. This was markedly greater than the difference in saline MD animals (-11.0 +/- 0.8 D). DPA MD animals showed a relative myopia of -14.3 +/- 2.2 D. The structural correlate of the myopia, elongation of the vitreous chamber in the deprived eyes relative to the control eyes, was significantly greater in the beta-APN MD animals 0.53 +/- 0.03 mm, which was not significantly different from the saline MD group. Thinning of the posterior sclera, but not the cornea, was observed in the deprived eyes of beta-APN treated tree shrews, along with a tessellated appearance to the fundus. The eyes of the beta-APN open animals showed no significant differences from normal. Beta-APN MD and DPA MD treated chickens did not develop greater myopia or vitreous chamber elongation than standard MD chickens. The selective effect of the lathyritic agents on the deprived eyes in tree shrew suggests that collagen crosslinking interacts, in the mammalian sclera, with a retinally-derived signal to regulate the elongation of the eye in myopia.

Aminopropionitrile↗
PubMed1996

The timing of thyroid-dependent programming in seasonally breeding male American tree sparrows (Spizella arborea).

There is convincing evidence that euthyroid male American tree sparrows are already programmed for seasonal reproduction and postnuptial molt by Week 4 of photostimulation. To explore more precisely when, during early photostimulation, thyroid-dependent programming of seasonal events occurs, photosensitive male tree sparrows were radiothyroidectomized or sham thyroidectomized on the first day of photostimulation (Week 0) or at Weeks 1 or 3 thereafter. Birds were monitored for testicular growth and regression over 8 or 12 weeks and then tested for photosensitivity or photorefractoriness by exposing them to constant light and exogenous L-thyroxine for 4 weeks. Molt of the primary flight feathers was scored periodically, and at the end of the experiment, hypothalami were saved for cGnRH-I (chicken gonadotropin-releasing hormone I) assay. Because (1) the thyroid is already dysfunctional by Day 4 after radiothyroidectomy, (2) thyroid-dependent photoinduced gonadal growth is programmed growth, and as demonstrated here, (3) testis length at Week 6 on long days (i.e., maximum or near-maximum testis size) is independent of the time of thyroidectomy at or after the onset of photostimulation, we conclude that male American tree sparrows were programmed for photoperiodic testicular growth during the first week of photostimulation. Based on measurements of testis length and hypothalamic cGnRH-I content, only 2 of 11 birds thyroidectomized at Week 1 were already programmed for photorefractoriness by Week 1, whereas all birds thyroidectomized at Week 3 were so programmed by Week 3. Marked differences in molt scores between photorefractory (thyroidectomized and euthyroid) and photosensitive (thyroidectomized) birds argue that postnuptial molt also was programmed roughly between Weeks 1 and 3. To explain these results, we ascribe organizational-like actions directly or indirectly to endogenous thyroid hormones and argue that the onset of photostimulation opens a window, during which time euthyroid male American tree sparrows are programmed for seasonality. A clear dissociation of photorefractoriness from photoperiodic testicular growth in birds thyroidectomized at Week 1 suggests that separate control circuits mediate these two annually periodic events.

Animals↗
PubMed1999

Long days and thyroxine program american tree sparrows for seasonality: evidence for temporal flexibility of the breeding season of euthyroid females.

To explore the role of the thyroid in the control of seasonality, photosensitive female American tree sparrows (Spizella arborea) were thyroidectomized (THX), moved to long days, and given daily injections of thyroxine (T4) for 3 weeks; THX and thyroid-intact (THI) controls received daily injections of alkaline vehicle. Birds were retained on long days 4 additional weeks and then moved to constant light and given T4 in drinking water for 5 weeks in order to test for photorefractoriness. Endpoints were ovarian mass, molt score, and hypothalamic cGnRH-I (chicken gonadotropin-releasing hormone I) content; data were collected as independent measures at intervals of 1 to 5 weeks. THX females given T4 replacement therapy (THXT4 females) exhibited all components of seasonality (i.e., photoperiodic ovarian growth, photorefractoriness, and postnuptial molt), as did THI females. THX females not given replacement T4 were aseasonal: They showed only minor thyroid-independent photoperiodic ovarian growth; they remained photosensitive, despite chronic photostimulation; and they did not initiate postnuptial molt. Collectively, these observations support, and extend to female tree sparrows, our model of seasonality in male tree sparrows, wherein control circuits are programmed for gonadal growth, photorefractoriness, and postnuptial molt by interactive effects of long days and thyroid hormone during the first 3 weeks of photostimulation. The unexpected finding that constant light and/or exogenous T4 extended the simulated breeding seasons of some THI females prompted us to investigate the nature and expression of photorefractoriness. Our approach was to evaluate the same endpoints as before in chronically photostimulated THI females either retained on long days, with or without T4 in drinking water, or moved to constant light, with or without T4. The results showed that exposure to constant light (not T4) near the end of a simulated breeding season can-though usually it does not-temporarily extend the breeding season and prevent the onset of postnuptial molt. It remains unclear whether these perturbations caused by constant light reflect a transitional relative photorefractoriness or merely a delay in the onset of absolute photorefractoriness. In either case, the thyroid- and daylength-dependent programs controlling seasonality in female American tree sparrows have a heretofore undemonstrated potential for limited temporal flexibility.

Animals↗
PubMed1994

Root probabilities for intraspecific gene trees under neutral coalescent theory.

The rooting of intraspecific gene or haplotype trees has proven to be difficult using the traditional techniques of rooting species trees such as outgroups. As an alternative, we apply neutral coalescent theory to the problems of determining the root of an intraspecific gene tree and the relative ages of the haplotypes. By using a recursive equation, exact root probabilities can be calculated for small cladograms and sample sizes. These exact probabilities indicate that root probabilities are not very sensitive to the parameter theta, which is four times the mutation rate times the inbreeding effective size. The exact probabilities also indicate that root probabilities are not very sensitive to the absolute numbers of each haplotype (allele) class, only their relative proportions. The exact method, unfortunately, is not feasible for implementation with larger data sets with present algorithms and computers. However, the exact results suggested a simple heuristic for determining outgroup weights; that is, finding the haplotype that is the oldest in the sample and that can serve as an outgroup for the remainder of the haplotype tree. Computer simulations revealed that these outgroup weights are strongly correlated with actual age and are much better indicators of haplotype age than is the haplotype frequency, another commonly used indicator of relative age.

Gene Frequency↗
PubMed1998

Phylogenetic utility of the external transcribed spacer (ETS) of 18S-26S rDNA: congruence of ETS and ITS trees of Calycadenia (Compositae).

The 3' region of the external transcribed spacer (ETS) of 18S-26S nuclear ribosomal DNA was sequenced in 19 representatives of Calycadenia/Osmadenia and two outgroup species (Compositae) to assess its utility for phylogeny reconstruction compared to rDNA internal transcribed spacer (ITS) data. Universal primers based on plant, fungal, and animal sequences were designed to amplify the intergenic spacer (IGS) and an angiosperm primer was constructed to sequence the 3' end of the ETS in members of tribe Heliantheae. Based on these sequences, an internal ETS primer useful across Heliantheae sensu lato was designed to amplify and sequence directly the 3' ETS region in the study taxa, which were the subjects of an earlier phylogenetic investigation based on ITS sequences. Size variation in the amplified ETS region varied across taxa of Heliantheae sensu lato from approximately 350 to 700 bp, in part attributable to an approximately 200-bp tandem duplication in a common ancestor of Calycadenia/Osmadenia. Phylogenetic analysis of the 200-bp subrepeats and examination of apomorphic changes in the duplicated region demonstrate that the subrepeats in Calycadenia/Osmadenia have evolved divergently. Phylogenetic analyses of the entire amplified ETS region yielded a highly resolved strict consensus tree that is nearly identical in topology to the ITS tree, with strong bootstrap and decay support on most branches. Parsimony analyses of combined ETS and ITS data yielded a strict consensus tree that is better resolved and generally better supported than trees based on either data set analyzed separately. We calculated an approximately 1.3- to 2.4-fold higher rate of sequence evolution by nucleotide substitution in the ETS region studied than in ITS-1 + ITS-2. A similar disparity in the proportion of variable (1.3 ETS:1 ITS) and potentially informative (1.5 ETS:1 ITS) sites was observed for the ingroup. Levels of homoplasy are similar in the ETS and ITS data. We conclude that the ETS holds great promise for augmenting ITS data for phylogenetic studies of young lineages.

Base Sequence↗
PubMed2000

Inference from gene trees in a subdivided population.

This paper studies gene trees in subdivided populations which are constructed as perfect phylogenies from the pattern of mutations in a sample of DNA sequences and presents a new recursion for the probability distribution of such gene trees. The underlying evolutionary model is the coalescent process in a subdivided population. The infinitely-many-sites model of mutation is assumed. Ancestral inference questions that are discussed are maximum likelihood estimation of migration and mutation rates; detection of population growth by likelihood techniques; determining the distribution of the time to the most recent common ancestor of a sample of sequences; determining the distribution of the age of the mutations on the gene tree; determining in which subpopulation the most recent common ancestor of all the sequences was; determining subpopulation ancestors, where they were, and times to them; and determining in which subpopulations mutations occurred. A computational technique of Griffiths and Tavaré used is a computer intensive Markov chain simulation, which simulates gene trees conditional on their topology implied by the mutation pattern in the sample of DNA sequences. The software GENETREE, which implements these ancestral inference techniques, is available.

Algorithms↗