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PubMed1986

Rates of nuclear DNA evolution in pheasant-like birds: evidence from restriction maps.

To examine the tempo of genomic evolution in birds, we mapped 161 restriction sites in the nuclear DNA of seven species of birds belonging to the pheasant superfamily Phasianoidea. The three regions mapped lie on different chromosomes and bear eight genes, coding for lysozyme c, three "alpha-like" globins, and four "beta-like" globins. Together, the three regions span about 56 kilobases, most of which is presumably noncoding. The maps differed from one another at a minimum of 77 sites and by 9 length mutations. The extent of sequence divergence due to base substitutions was inferred to be similar for all three regions, even though the three coding regions differ by 5-fold from one another in mean rate of evolution at the amino acid level. A tree relating the maps differs in branching order from that implied by the traditional classification of phasianoid birds and is supported by published protein comparisons. Five of the nodes in the tree were associated with fossil evidence and historical biogeographic information, allowing us to estimate the mean rate of DNA divergence to be 0.34-0.40% per million years. This rate is similar to that estimated for the globin gene regions of higher primates, which validates the concept of an evolutionary clock at the DNA level. Our fossil-based calibration of DNA evolution differs by a factor of almost 2 from that proposed by others on the basis of biogeography. In consequence, published estimates of divergence times for birds and primates that are based on a biogeographically calibrated DNA clock may be too long.

Animals↗
PubMed1988

Colonization of the Krakatau Islands by vertebrates: equilibrium, succession, and possible delayed extinction.

MacArthur and Wilson [MacArthur, R. H. & Wilson, E. O. (1967) The Theory of Island Biogeography (Princeton Univ. Press, Princeton, NJ)] used the rate of recolonization of the Krakatau Islands (sterilized in the cataclysmic 1883 eruption) by birds and vascular plants to test their equilibrium model of immigration and extinction processes on islands. Working with data only up to 1933, they concluded that the number of resident land bird species had approached equilibrium by 1908-1919, 25-36 years after the eruption, when the number of vascular plant species was still increasing. Recent surveys of vertebrates on the archipelago show continuing colonization, as well as species turnover. Nonmigrant nonmarine birds and reptiles are only now approaching equilibrium species numbers; archipelago acquisition rates for these groups are lower than in the 40 years following the 1883 eruption. Apparent (minimal) annual extinction rates are an order of magnitude lower than those calculated for equilibrium by MacArthur and Wilson. The active volcano Anak Krakatau emerged in 1930 and suffered an eruption in 1952 that destroyed the vegetation. It is still at an early stage of succession and on the threshold of major vegetational change. This island and a physically dynamic, ever-young spit on Sertung I, also held at an early successional stage, may provide (i) ecological refuges for some species whose optimal habitat on the older islands is being extirpated by vegetational succession and (ii) ecological "windows" through which such species may still establish from the mainland, thus postponing their extinction on the archipelago.

Animals↗
PubMed1992

An rbcL sequence from a Miocene Taxodium (bald cypress).

During the past decade, ancient DNAs from both animals and plants have been successfully extracted and analyzed. Recently, the age of DNA that can be recovered and sequenced was increased manyfold by the amplification and sequencing of a DNA fragment from a Magnolia fossil obtained from the Miocene Clarkia deposit (17-20 million yr old). However, the validity of this report has been questioned based on models predicting that DNA should be completely degraded after 4 million yr. We report here the successful amplification, sequencing, and analysis of a 1320-base-pair portion of the chloroplast gene rbcL from a Miocene Taxodium specimen, also from the Clarkia site. These data not only validate the earlier report of sequence data for a Magnolia species from the same site but also suggest that it may be possible to isolate and sequence DNAs routinely from the Clarkia deposit. The ability to recover and sequence DNAs of such age offers enormous research possibilities in the areas of molecular evolution, biogeography, and systematics.

Base Sequence↗
PubMed1997

Primate species richness is determined by plant productivity: implications for conservation.

The explanation of patterns in species richness ranks among the most important tasks of ecology. Current theories emphasize the interaction between historical and geographical factors affecting the size of the regional species pool and of locally acting processes such as competitive exclusion, disturbance, productivity, and seasonality. Local species richness, or alpha diversity, of plants and primary consumers has been claimed to peak in habitats of low and intermediate productivity, which, if true, has major implications for conservation. Here, by contrast, we show that local richness of Neotropical primates (platyrrhines) is influenced by both historical biogeography and productivity but not by tree species richness or seasonality. This pattern indicates that habitats with the highest plant productivity are also the richest for many important primary consumers. We show further that fragmentation of Amazonian rain forests in the Pleistocene, if it occurred, appears to have had a negligible influence on primate alpha species richness.

Animals↗
PubMed1998

Tarsier-like locomotor specializations in the oligocene primate afrotarsius.

Tarsiers and extinct tarsier-like primates have played a central role in views of primate phylogeny and evolution for more than a century. Because of the importance of tarsiers in so many primatological problems, there has been particular interest in questions about the origin of tarsier specializations and the biogeography of early tarsioid radiations. We report on a new fossil of rare Afrotarsius that shows near identity to modern Tarsius in unique specializations of the leg, which provides information about the locomotor behavior and clarifies the phylogenetic position of this previously controversial primate. These specializations constitute evidence that Afrotarsius is a tarsiid, closely related to extant Tarsius; hence, it is now excluded from being a generalized sister taxon to Anthropoidea.

Animals↗
PubMedDate not supplied

On areas of endemism, with an example from the African Restionaceae.

Areas of endemism are central to cladistic biogeography. The concept has been much debated in the past, and from this has emerged the generally accepted definition as an area to which at least two species are endemic. Protocols for locating areas of endemism have been neglected, and to date no attempt has been made to develop optimality criteria against which to evaluate competing hypotheses of areas of endemism. Here various protocols for finding areas of endemism are evaluated--protocols based on both phonetic and parsimony analyses, on both unweighted data and data weighted by various criteria. The optimality criteria used to compare the performance of the methods include the number of species included in the areas of endemism, the number of areas delimited, and the degree of distributional congruency of the species restricted to each area of endemism. These methods are applied to the African Restionaceae in the Cape Floristic Region. Parsimony methods using weighted data are shown to perform best on the combination of all three optimality criteria. By varying the weighting parameters, the size of the areas of endemism can be varied. This provides a very useful tool for locating areas of endemism that satisfy prespecified scale criteria.

Demography↗
PubMed2002

Geographic origin of human mitochondrial DNA: accommodating phylogenetic uncertainty and model comparison.

Many biogeographic problems are tested on phylogenetic trees. Typically, the uncertainty in the phylogeny is not accommodated when investigating the biogeography of the organisms. Here we present a method that accommodates uncertainty in the phylogenetic trees. Moreover, we describe a simple method for examining the support for competing biogeographic scenarios. We illustrate the method using mitochondrial DNA sequences sampled from modern humans. The geographic origin of modern human mtDNA is inferred to be in Africa, although support for this hypothesis was ambiguous for data from an early paper.

Africa↗
PubMed2002

Phylogenetic placement of retropinnid fishes: data set incongruence can be reduced by using asymmetric character state transformation costs.

We used mitochondrial DNA sequences to determine the phylogenetic placement of southern smelts (Retropinnidae), a group of diadromous fishes endemic to New Zealand and Australia. Our genetic data strongly support a sister group relationship between retropinnids and northern hemisphere smelts (Osmeridae), a relationship that seems consistent with the similar appearance and life history strategies of these two groups. Our analysis indicates that Retropinnidae and Osmeridae together represent the sister group to the southern hemisphere galaxiid fishes (Galaxiidae). However, this finding conflicts with several recent osteological analyses, which supported a sister relationship for Retropinnidae and Galaxiidae, giving a monophyletic southern hemisphere assemblage (Galaxioidea). We review cases of incongruence and discuss factors that might explain significant disagreement between molecular and morphological data matrices. We suggest that repeated evolutionary simplification may have undermined the accuracy of morphological hypotheses of osmeroid relationships. Although equally weighted parsimony analysis of morphological data rejects the molecular hypothesis (Osmeridae + Retropinnidae), implementation of a range of weighting schemes suggests that incongruence is nonsignificant under asymmetric character transformation models. We propose that a simple "equal transformation cost" parsimony analysis may be biologically unrealistic, especially when reductive homoplasy is widespread; as is increasingly being accepted, complex character states are more readily lost than gained. Therefore, we recommend that morphological systematists routinely implement a range of character transformation models to assess the sensitivity of their phylogenetic reconstructions. We discuss the antitropical biogeography of osmeroid fishes in the context of vicariance and transequatorial dispersal.

Animals↗
PubMed2006

The pattern and timing of diversification of Philippine endemic rodents: evidence from mitochondrial and nuclear gene sequences.

The 22 genera and 64 species of rodents (Muridae: Murinae) distributed in the Philippine Islands provide a unique opportunity to study patterns and processes of diversification in island systems. Over 90% of these rodent species are endemic to the archipelago, but the relative importance of dispersal from the mainland, dispersal within the archipelago, and in situ differentiation as explanations of this diversity remains unclear, as no phylogenetic hypothesis for these species and relevant mainland forms is currently available. Here we report the results of phylogenetic analyses of the endemic Philippine murines and a wide sampling of murine diversity from outside the archipelago, based on the mitochondrial cytochrome b gene and the nuclear-encoded IRBP exon 1. Analysis of our combined gene data set consistently identified five clades comprising endemic Philippine genera, suggesting multiple invasions of the archipelago. Molecular dating analyses using parametric and semiparametric methods suggest that colonization occurred in at least two stages, one ca. 15 Mya, and another 8 to 12 million years later, consistent with the previous recognition of "Old" and "New" endemic rodent faunas. Ancestral area analysis suggests that the Old Endemics invaded landmasses that are now part of the island of Luzon, whereas the three New Endemic clades may have colonized through either Mindanao, Luzon, or both. Further, our results suggest that most of the diversification of Philippine murines took place within the archipelago. Despite heterogeneity between nuclear and mitochondrial genes in most model parameters, combined analysis of the two data sets using both parsimony and likelihood increased phylogenetic resolution; however, the effect of data combination on support for resolved nodes was method dependent. In contrast, our results suggest that combination of mitochondrial and nuclear data to estimate relatively ancient divergence times can severely compromise those estimates, even when specific methods that account for rate heterogeneity among genes are employed. [Biogeography; divergence date estimation; mitochondrial DNA; molecular systematics; Murinae; nuclear exon; Philippines; phylogeny.].

Animals↗
PubMed2005

Archaeobatrachian paraphyly and pangaean diversification of crown-group frogs.

Current models for the early diversification of living frogs inferred from morphological, ontogenetic, or DNA sequence data invoke very different scenarios of character evolution and biogeography. To explore central controversies on the phylogeny of Anura, we analyzed nearly 4000 base pairs of mitochondrial and nuclear DNA for the major frog lineages. Likelihood-based analyses of this data set are congruent with morphological evidence in supporting a paraphyletic arrangement of archaeobatrachian frogs, with an (Ascaphus + Leiopelma) clade as the sister-group of all other living anurans. The stability of this outcome is reinforced by screening for phylogenetic bias resulting from site-specific rate variation, homoplasy, or the obligatory use of distantly related outgroups. Twenty-one alternative branching and rooting hypotheses were evaluated using a nonparametric multicomparison test and parametric bootstrapping. Relaxed molecular clock estimates situate the emergence of crown-group anurans in the Triassic, approximately 55 million years prior to their first appearance in the fossil record. The existence of at least four extant frog lineages on the supercontinent Pangaea before its breakup gains support from the estimation that three early splits between Laurasia- and Gondwana-associated families coincide with the initial rifting of these landmasses. This observation outlines the potential significance of this breakup event in the formation of separate Mesozoic faunal assemblages in both hemispheres.

Animals↗
PubMed2006

That awkward age for butterflies: insights from the age of the butterfly subfamily Nymphalinae (Lepidoptera: Nymphalidae).

The study of the historical biogeography of butterflies has been hampered by a lack of well-resolved phylogenies and a good estimate of the temporal span over which butterflies have evolved. Recently there has been surge of phylogenetic hypotheses for various butterfly groups, but estimating ages of divergence is still in its infancy for this group of insects. The main problem has been the sparse fossil record for butterflies. In this study I have used a surprisingly good fossil record for the subfamily Nymphalinae (Lepidoptera: Nymphalidae) to estimate the ages of diversification of major lineages using Bayesian relaxed clock methods. I have investigated the effects of varying priors on posterior estimates in the analyses. For this data set, it is clear that the prior of the rate of molecular evolution at the ingroup node had the largest effect on the results. Taking this into account, I have been able to arrive at a plausible history of lineage splits, which appears to be correlated with known paleogeological events. The subfamily appears to have diversified soon after the K/T event about 65 million years ago. Several splits are coincident with major paleogeological events, such as the connection of the African and Asian continents about 21 million years ago and the presence of a peninsula of land connecting the current Greater Antilles to the South American continent 35 to 33 million years ago. My results suggest that the age of Nymphalidae is older than the 70 million years speculated to be the age of butterflies as a whole.

Animals↗
PubMed2005

Patterns of cladogenesis in the venomous marine gastropod genus Conus from the Cape Verde islands.

Isolated oceanic archipelagos are excellent model systems to study speciation, biogeography, and evolutionary factors underlying the generation of biological diversity. Despite the wealth of studies documenting insular speciation, few of them focused on marine organisms. Here, we reconstruct phylogenetic relationships among species of the marine venomous gastropod genus Conus from the Cape Verde archipelago. This small island chain located in the Central Atlantic hosts 10% of the worldwide species diversity of Conus. Analyses were based on mtDNA sequences, and a novel nuclear marker, a megalin-like protein, member of the low-density lipoprotein receptor gene family. The inferred phylogeny recovered two well-defined clades within Conus. One includes Cape Verde endemic species with larger shells, known as the "venulatus" complex together with C. pulcher from the Canary Islands. The other is composed of Cape Verde endemic and West Africa and Canary Island "small" shelled species. In both clades, nonendemic Conus were resolved as sister groups of the Cape Verde endemics, respectively. Our results indicate that the ancestors of "small" and "large" shelled lineages independently colonized Cape Verde. The resulting biogeographical pattern shows the grouping of most Cape Verde endemics in monophyletic island assemblages. Statistical tests supported a recent radiation event within the "small shell" clade. Using a molecular clock, we estimated that the colonization of the islands by the "small" shelled species occurred relatively close to the origin of the islands whereas the arrival of "large" shelled Conus is more recent. Our results suggest that the main factor responsible for species diversity in the archipelago may be allopatric speciation promoted by the reduced dispersal capacity of nonplanktonic lecithotrophic larvae.

Africa, Western↗
PubMed1998

Weighted ancestral area analysis and a solution of the redundant distribution problem.

A new cladistic method for the estimation of ancestral areas is based on reversible parsimony in combination with a weighting scheme that weights steps in positionally plesiomorphic branches more highly than steps in positionally apomorphic branches. By applying this method to cladograms of human mitochondrial DNA, the method is superior to previously proposed algorithms. The method is also an appropriate tool for the solution of the redundant distribution problem in area cladograms. Under the assumption of allopatric speciation, redundant distributions, i.e., sympatry of sister groups, show that dispersal has occurred; thus, the ancestral area of at least one sister group was smaller than the combined distribution of its descendants. With the weighted ancestral area analysis, the ancestral areas can be confined and at least some dispersal events can be distinguished from possible vicariance events. As applied to a cladogram of the Polypteridae, weighted ancestral area analysis is superior to Brooks parsimony analysis (assumption 0) and component analysis under assumptions 1 and 2 (Nelson and Platnick, 1981, Systematics and biogeography: Cladistics and vicariance. Columbia Univ. Press, New York.) in resolving redundancies. The results of the weighted ancestral area analysis may differ from the results of dispersal-vicariance analysis, because the rules of dispersal-vicariance analysis indirectly favor the questionable assumption that the ancestral species occupied only one unit area.

Algorithms↗
PubMedDate not supplied

Ascospore diversity of bryophilous Hypocreales and two new hepaticolous Nectria species.

Hypocreales represents one of the most successful orders of ascomycetes on mosses and hepatics, and more than 30 obligately bryophilous species belonging to seven genera of Bionectriaceae and Nectriaceae are known. These fungi have a remarkably wide range of ascospore types that differ in form, size and septation. Especially heterogeneous are the ascospores of the six hypocrealean parasites recorded on European populations of Frullania dilatata. Patterns of distribution of bryophilous Hypocreales on this host appear to follow the principles of island biogeography. Two new leaf-perforating species of Nectria with unusual ascospores are described. Nectria foertheri Döbbeler sp. nov. grows biotrophically on Porella sp. in Guatemala, and N. lagodes Döbbeler sp. nov. is a necrotroph on Frullania dilatata in Italy and Greece.

Hepatophyta↗
PubMed2004

History and the species-area relationship in Lesser Antillean birds.

We examined the species-area relationship for three historically distinct subsets of Lesser Antillean birds identified by molecular phylogenetic analysis of island and continental populations. The groups comprised recent colonists from continental or Greater Antillean source populations, old taxa having recently expanded distributions within the Lesser Antilles, and old endemic taxa lacking evidence of recent dispersal between islands. The number of young taxa was primarily related to distance from the source of colonists in South America. In a multiple regression, the logarithmic slope of the species-area relationship for this group was shallow (0.066+/-0.016). Old endemic taxa were restricted to islands with high elevation, and within this subset, species richness was related primarily to island area, with a steep slope (0.719+/-0.110). The number of recently spread endemic taxa was related primarily to island elevation, apparently reflecting the persistence of such populations on islands with large areas of forested and montane habitats. Historical analysis of the Lesser Antillean avifauna supports the dynamic concept of island biogeography of MacArthur and Wilson, rather than the more static view of David Lack, in that colonists exhibit dispersal limitation and extinction plays a role in shaping patterns of diversity. However, the avifauna of the Lesser Antilles is probably not in equilibrium at present, and the overall species-area relationship might reflect changing proportions of historically distinguishable subsets of species.

Animals↗
PubMed2004

What is speciation and how should we study it?

To understand speciation, we first need to know what species are. Yet debates over species concepts have seemed endless, with little obvious relevance to the study of speciation. Recently, there has been progress in resolving these debates, favoring a lineage-based, evolutionary species concept. This progress calls for reconsideration of the study of speciation. Traditional speciation research based on the biological species concept has led to great advances in understanding how nonallopatric speciation occurs and how species diverge and remain separate from each other. However, this research has neglected the question of how new species arise in the first place for the most common geographic mode (allopatric). A new and very different research program is needed to understand the ecological and evolutionary processes that split an ancestral species into new allopatric lineages. This research program will connect speciation to many other fundamental questions in evolutionary biology, ecology, biogeography, and conservation biology.

Animals↗
PubMed1991

Environmental sex determination in reptiles: ecology, evolution, and experimental design.

Sex-determining mechanisms in reptiles can be divided into two convenient classifications: genotypic (GSD) and environmental (ESD). While a number of types of GSD have been identified in a wide variety of reptilian taxa, the expression of ESD in the form of temperature-dependent sex determination (TSD) in three of the five major reptilian lineages has drawn considerable attention to this area of research. Increasing interest in sex-determining mechanisms in reptiles has resulted in many data, but much of this information is scattered throughout the literature and consequently difficult to interpret. It is known, however, that distinct sex chromosomes are absent in the tuatara and crocodilians, rare in amphisbaenians (worm lizards) and turtles, and common in lizards and snakes (but less than 20% of all species of living reptiles have been karyotyped). With less than 2 percent of all reptilian species examined, TSD apparently is absent in the tuatara, amphisbaenians and snakes; rare in lizards, frequent in turtles, and ubiquitous in crocodilians. Despite considerable inter- and intraspecific variation in the threshold temperature (temperature producing a 1:1 sex ratio) of gonadal sex determination, this variation cannot confidently be assigned a genetic basis owing to uncontrolled environmental factors or to differences in experimental protocol among studies. Laboratory studies have identified the critical period of development during which gonadal sex determination occurs for at least a dozen species. There are striking similarities in this period among the major taxa with TSD. Examination of TSD in the field indicates that sex ratios of hatchlings are affected by location of the nests, because some nests produce both sexes whereas the majority produce only one sex. Still, more information is needed on how TSD operates under natural conditions in order to fully understand its ecological and conservation implications. TSD may be the ancestral sex-determining condition in reptiles, but this result remains tentative. Physiological investigations of TSD have clarified the roles of steroid hormones, various enzymes, and H-Y antigen in sexual differentiation, whereas molecular studies have identified several plausible candidates for sex-determining genes in species with TSD. This area of research promises to elucidate the mechanism of TSD in reptiles and will have obvious implications for understanding the basis of sex determination in other vertebrates. Experimental and comparative investigations of the potential adaptive significance of TSD appear equally promising, although much work remains to be performed. The distribution of TSD within and among the major reptilian lineages may be related to the life span of individuals of a species and to the biogeography of these species.(ABSTRACT TRUNCATED AT 400 WORDS)

Animals↗
PubMed2004

Convergence, divergence, and homogenization in the ecological structure of emydid turtle communities: the effects of phylogeny and dispersal.

Studies that have explored the origins of patterns of community structure from a phylogenetic perspective have generally found either convergence (similarity) in community structure between regions through adaptive evolution or lack of convergence (dissimilarity) due to phylogenetic conservatism in the divergent ecological characteristics of lineages inhabiting different regions. We used a phylogenetic approach to document a third pattern in the structure of emydid turtle communities. Emydid communities in southeastern North America tend to have a higher proportion of aquatic species than those in the northeast. This pattern reflects phylogenetic conservatism in the ecology and biogeography of two basal emydid clades, limiting convergence in community structure between these regions. However, differences in community structure between northeastern and southeastern North America have also been homogenized considerably by the dispersal of species with phylogenetically conserved ecological characteristics between regions. This pattern of ecologically conservative dispersal may be important in many continental and oceanic systems.

Animals↗