James S. Rogers

Bias in phylogenetic estimation and its relevance to the choice between parsimony and likelihood methods.

DAVID L. SWOFFORD,1,6 PETER J. WADDELL,2 JOHN P. HUELSENBECK,3 PETER G. FOSTER,1,7 PAUL O. LEWIS,4 AND JAMES S. ROGERS5 Laboratory of Molecular Systematics, National Museum of Natural History, Smithsonian Institution Museum Support Center, 4210 Silver Hill Road, Suitland, Maryland 20746, USA; E-mail: swofford@lms.si.edu Institute of Molecular BioSciences, Massey University, Palmerston North, New Zealand; E-mail: waddell@onyx.si.edu Department of Biology, University of Rochester, Rochester, New York 14627, USA; E-mail: johnh@brahms.biology.rochester.edu Department of Ecology and Evolutionary Biology, The University of Connecticut, U-43, 75 N. Eagleville Road, Storrs, Connecticut 06269-30437 , USA; E-mail: plewis@uconnvm.uconn.edu Department of Biological Sciences, University of New Orleans, New Orleans, Louisiana 70148, USA; E-mail: jsrogers@uno.edu

Maximum Likelihood Estimation of Phylogenetic Trees Is Consistent When Substitution Rates Vary According to the Invariable Sites plus Gamma Distribution

Maximum likelihood estimation of phylogenetic trees from nucleotide sequences is completely consistent when nucleotide substitution is governed by the general time reversible (GTR) model with rates that vary over sites according to the invariable sites plus gamma (I + gamma) distribution.

A Discriminant Functions Analysis of Sunfish (Lepomis) Food Habits and Feeding Niche Segregation in the Lake Pontchartrain, Louisiana Estuary

Abstract The food habits of four species of sunfish, Lepomis macrochirus, L. microlophus, L. punctatus, and L. gulosus were studied in the Lake Pontchartrain estuary. Forty estuarine food items were identified from stomach samples. Although the food items were different from those of Lepomis spp. in fresh water, specific feeding patterns in regard to prey size and space partitioning were comparable. A discriminant functions analysis was used to objectively compare specific differences in stomach content data. Differences in discriminant function scores appeared to be due to interspecific feeding niche segregation.

CENTRAL MOMENTS AND PROBABILITY DISTRIBUTION OF COLLESS'S COEFFICIENT OF TREE IMBALANCE

The great increase in the number of phylogenetic studies of a wide variety of organisms in recent decades has focused considerable attention on the balance of phylogenetic trees—the degree to which sister clades within a tree tend to be of equal size—for at least two reasons: (1) the degree of balance of a tree may affect the accuracy of estimates of it; (2) the degree of balance, or imbalance, of a tree may reveal something about the macroevolutionary processes that produced it. In particular, variation among lineages in rates of speciation or extinction is expected to produce trees that are less balanced than those that result from phylogenetic evolution in which each extant species of a group has the same probability of speciation or extinction. Several coefficients for measuring the balance or imbalance of phylogenetic trees have been proposed. I focused on Collesss coefficient of imbalance (7) for its mathematical tractability and ease of interpretation. Earlier work on this statistic produced exact methods only for calculating the expected value. In those studies, the variance and confidence limits, which are necessary for testing the departure of observed values of I from the expected, were estimated by Monte Carlo simulation. I developed recursion equations that allow exact calculation of the mean, variance, skewness, and complete probability distribution of I for two different probability‐generating models for bifurcating tree shapes. The Equal‐Rates Markov (ERM) model assumes that trees grow by the random speciation and extinction of extant species, with all species that are extant at a given time having the same probability of speciation or extinction. The Equal Probability (EP) model assumes that all possible labeled trees for a given number of terminal taxa have the same probability of occurring. Examples illustrate how these theoretically derived probabilities and parameters may be used to test whether the evolution of a monophyletic group or set of monophyletic groups has proceeded according to a Markov model with equal rates of speciation and extinction among species, that is, whether there has been significant variation among lineages in expected rates of speciation or extinction.

Allozyme evidence for crane systematics and polymorphisms within populations of Sandhill, Sarus, Siberian, and whooping cranes

Electrophoretic analysis of proteins yielded evidence on the relationships of species of cranes and on genetic diversity within populations of some species. Diversity within the Greater Sandhill crane and a Florida population of the Florida Sandhill crane was similar to that of most other vertebrates, but diversity was low in the Mississippi Sandhill crane, in the Okefenokee population of the Florida Sandhill crane, and within the Siberian and Sarus cranes. Diversity was surprisingly high among whooping cranes, whose number dropped to less than 25 early in this century. Phylogenetic analysis, using both character state and distance algorithms, yielded highly concordant trees for the 15 species. The African crowned cranes (Balearica) were widely divergent from all other cranes. Species of Anthropoides, Bugeranus, and Grus clustered closely but sorted into two lineages: a Whooper Group consisted of the whooping, common, hooded, black-necked, white-naped, and red-crowned cranes of genus Grus; and a Sandhill Group included the Sandhill, Siberian, Sarus, and Brolga cranes of genus Grus, the wattled crane of genus Bugeranus, and the Demoiselle and blue cranes of genus Anthropoides.

Biochemical Systematics of the Notropis roseipinnis Complex (Cyprinidae: Subgenus Lythrurus)

Ce complexe renferme 4 taxas distribues dans le sud-est des Etats-Unis: Notropis roseipinnis, N. atrapiculus, N.b. bellus, N.b. alegnotus

Species Density and Taxonomic Diversity of Texas Amphibians and Reptiles

Rogers, J. S. (Department of Biological Sciences, University of New Orleans, New Orleans, Louisiana 70122) 1976. Species density and taxonomic diversity. of Texas amphibians and reptiles. Syst. Zool. 25:26-40.-Species densities of Texas amphibians and . reptiles are highly correlated with several components of the physical environment. Multiple regression and partial correlation analyses of these relationships lead to several conclusions: 1) species densities of salamanders, frogs, turtles, lizards, and snakes increase significantly with increasing topographic relief, probably because of the greater number of habitat types that occur in uneven terrain versus flat terrain; 2) altitude, per se, has a negative effect upon species densities of all five groups, especially lizards and snakes; 3) species densities of salamanders and turtles increase with increasing mean annual precipitation, either because of increasing productivity or increasing numbers of aquatic habitats; 4) mean annual temperature and growing season have significant effects on species densities only for salamanders, temperature having a positive effect and growing season a negative effect; 5) with a few exceptions, seasonality and year-to-year variability of climatic factors are not correlated with species densities; and 6) species densities of snakes and, to a lesser degree, lizards increase with increasing species density of small mammals. The mean number of species per genus in each of the five groups of Texas amphibians and reptiles also exhibits considerable geographical variation. Much of this variation is caused by variation in species densities, since species per genus and species density are strongly positively -correlated. However, even after this correlation is statistically removed there is extensive geographical variation of numbers of species per genus. Some of this variation can be accounted for by environmental influences: 1) species per genus of frogs and snakes increase significantly with increasing mean annual precipitation, possibly due to increasing uniformity of habitats and 2) species per genus of frogs and, to a smaller degree, snakes increase with increasing altitude. This may be related to decreasing productivity of food resources with increasing altitude. Dauring the past decade geographical variation in species density (numbers of species per unit area) of North American vertebrates has received considerable attention (Simpson, 1964; Cook, 1969; Kiester, 1971; Wilson, 1974). Each of the researchers who have studied this problem has proposed causal relationships between species density and various environmental factors, including topographic relief, altitude and climate. However, only one (Wilson, 1974) attempted to analyze these possible relationships statistically. The lack of statistical analyses would seem a serious deficiency, because of strong correlations between many environmental variables. Another possible complicating factor is history. This might be especially serious when considering a large area such as North America, where northem parts were glaciated rather recently and southern extremes have probably never been glaciated. Is the paucity of species of some vertebrate groups in the north due to present climatic conditions, to insufficient time having elapsed for recovery from the.. last glacial advance, or to a combination of these factors? In the present .study I attempt to, deal with the first problem by analyzing relationships between species density and several environmental vari-ables using multivariate statistical techniques. Secondly, to reduce the effect of history, I confined the study to a much smaller geographical area (the state . of Texas), but one with sufficient variation in species density and environmental parameters to yield interesting re-

Speciation with Little Genic and Morphological Differentiation in the Ribbon Snakes Thamnophis proximus and T. sauritus (Colubridae)

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Fundulus bifax, a New Species of the Subgenus Xenisma from the Tallapoosa and Coosa River Systems of Alabama and Georgia

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Evolutionary and Biogeographic Relationships of Fundulus catenatus (Fundulidae)

Evolutionary relationships among 21 geographic samples of the northern studfish, Fundulus catenatus, were inferred from genotype distributions at 24 presumptive gene loci. Phylogenetic treatment of allozymic data support a widespread ancestral distribution for the species in the region of the Central Highlands. Allozymic data further support a primary divergence between a Cumberland, Green, and Tennessee River segment of this ancestral distribution and an Indiana, lower Mississippi River, Ouachita, and Ozark population. Disjunct populations extant in the Ouachita Uplands represent an early divergence from an Indiana-Ozark-lower Mississippi River lineage. The White River, Indiana, and Ozark populations remain close relatives, with the lower Mississippi River populations diverging from this lineage. The inferred pattern of relationships is generally consistent with predictions based on recent hypotheses concerning the historical biogeography of the Central Highlands. One noteworthy point of divergence concerns the apparent close relationship between Ozark and Indiana populations. Such a pattern of relationship supports the persistence of gene flow across the region that is now the Central Lowlands after isolation of the Ouachita Highlands.