Methods in Vicariance Biogeography: Assessment of the Implementations of Assumptions 0, 1, and 2

As we have argued previously, for the valid derivation of general area cladograms in vicariance biogeography, two requirements should be met. First, sets of area cladograms derived under assumptions 0, 1 and 2 should be inclusive (requirement I). Second, general area cladograms should be based on area cladograms, for different monophyletic groups, derived under the same assumption (requirement II). We now assess for their actual implementation of assumptions A0, A1, and A2 and for the extent to which they meet requirements I and II, the following methods (and correlated computer programs): Component Compatibility Analysis (CAFCA), Brooks Parsimony Analysis (PAUP), Component Analysis (Component 1.5), Reconciled Tree Analysis (Component 2.0), and Three Area Statement Analysis (TAS). For this purpose we use empirical ( Heterandria, Xiphophorus, Cyttaria, Eriococcus/Madarococcus ) and theoretical data sets. All programs appear to violate, to a different degree, requirement I (deriving inclusive sets of area cladograms under assumptions) when dealing with sympatric taxa under A1 or A2. Dealing with sympatric taxa a posteriori only prevents this violation. All programs examined appear to meet requirement II (deriving general area cladograms under a single assumption).     

A Posteriori and a Priori Methodologies for Testing Hypotheses of Causal Processes in Vicariance Biogeography

Methods used in vicariance biogeography fall into the categories of a posteriori methods (e.g., Component Compatibility Analysis and Brooks Parsimony Analysis) and a priori methods (e.g., Component Analysis, Reconciled Tree Analysis, and Three Area Statement Analysis). Each category corresponds to a particular methodology that arrives at general area cladograms by testing null hypotheses in a particular way. A posteriori methods assume the process of vicariance only (A0) as a common cause of the distribution of different monophyletic groups of taxa under the null hypothesis. Whenever a parsimony analysis of combined data from these monophyletic groups results in a general area cladogram with homoplasy, the null hypothesis is rejected and extinction and dispersal are invoked a posteriori as ad hoc process explanations. A priori methods assume not only vicariance (A0) but also combinations of vicariance with the processes of extinction (A1) and dispersal (A2) as possible causes of the distribution of the taxa of different monophyletic groups. Each assumed set of processes corresponds to a different null hypothesis. Under the assumption of independence and thus additivity of the processes involved, the sets of area cladograms obtained under A0, A1, and A2 from data of each monophyletic group must be inclusive (requirement I). Whenever no congruent area cladograms are found in the intersection of sets of area cladograms derived under the same assumption for different monophyletic groups (II), the corresponding null hypothesis is rejected.     

Measures for Obtaining Inclusive Sets of Area Cladograms under Assumptions Zero, 1, and 2 with Different Methods for Vicariance Biogeography

We present modifications to computer programs of a posteriori and a priori methods for vicariance biogeography that enable them to obtain inclusive sets of area cladograms under assumptions zero, 1, and 2. With CAFCA (Component Compatibility Analysis) an upper limit for area cladogram selection by the number of steps is not always sufficient for inclusive sets. CAFCA needs additionally a lower limit for the number of components used to derive area cladograms when noninclusion arises because CAFCA selects area cladograms with different resolutions. PAUP (Brooks Parsimony Analysis) derives inclusive sets when it selects area cladograms under assumptions zero, 1, and 2 by using an upper limit for the number of steps and not collapsing unsupported nodes. For the computer programs Component 1.5 (Component Analysis), Component 2.0 (Reconciled Tree Analysis), and TAS (Three Area Statement Analysis) we suggest a two-step procedure for inclusive sets. The first step involves dealing with widespread taxa a priori under assumptions zero, 1, or 2. The second step involves dealing with sympatric taxa "as is" (Component 1.5 and TAS) or by tree reconciliation using an upper limit for the number of losses (Component 2.0).     

IN SEARCH OF A METHOD FOR CLADISTIC BIOGEOGRAPHY: AN EMPIRICAL COMPARISON OF COMPONENT ANALYSIS, BROOKS PARSIMONY ANALYSIS, AND THREE-AREA STATEMENTS

Abstract— Three quantitative cladistic biogeographic methods, namely, component analysis, Brooks parsimony analysis (BPA), and three-area statements (TAS) have been proposed for obtaining general area cladograms from taxon-area cladograms. Available programs implementing these methods include COMPONENT versions 1.5 and 2.0 for component analysis, TAS for three-area statements, and Hennig86 for analysing matrices for both three-area statements and BPA. Ten different data sets were analysed with these programs and items of error were used to evaluate the general area cladograms obtained. None of the computer implementations of the methods compared proved to be more effective than the others.
"…all methodologies, even the most obvious ones, have their limits…"
Feyerabend (1993:231)     

A CLADISTIC ANALYSIS OF CIRCAEA (ONAGRACEAE)

Abstract— Circaea (Onagraceae), a genus of seven species from the northern hemisphere, forms a monophylctic group defined by the following synapomorphies: two stamens (opposite the sepals), fruits indehiscent capsules, hooked hairs on the fruits, and perianth parts reduced to two. A cladistic analysis of the genus was performed using 22 characters from morphology, anatomy and palynology. The seven species and seven additional subspecies were considered the terminal taxa. Polarity of the characters is based on the outgroup comparison method. Eighteen equally parsimonious cladograms were produced, each with 32 steps and a consistency index of 0.75. A successive weighting procedure was applied, resulting in six cladograms with a consistency index of 0.95. All 24 cladograms share the following seven monophylctic groups: (1) all species except C. cordala and C. glabrescens (stipules deciduous); (2) the group of C. mollis , the three subspecies of C. lutetiana and C. erubescens (exsertcd nectary); (3) C. repens and all six subspecies of C. alpina (single-seeded fruits, stolons terminated by tubers, and viscin threads reduced or absent); (4) the six subspecies of C. alpina (unilocular ovaries with no trace of a second loculc and tardily opening perianth); (5) C. alpina subspecies alpina, micrantha, pacifica , and imaicola (flowers opening on ascending to erect pedicels); (6) C. alpina subspecies alpina, micrantha , and pacifica (translucent leaves); (7) C. alpina subspecies alpina and murantha (glabrous stems). Results of the cladistic analysis support most of the current systematic classification of the genus, except for the relationships among the three subspecies of C. lutetiana .     

Cladistic analysis and biogeography of the cicadas of the Indo-Pacific subtribe Cosmopsaltriina (Hemiptera: Cicadoidea: Cicadidae)

Abstract A consensus cladogram is presented for ninety-seven of the ninety-nine (sub)species of the cicada subtribe Cosmopsaltriina on the basis of a cladistic analysis of forty-nine characters. The consensus cladogram confirms the monophyly of the eight genera constituting the subtribe, and the monophyly of the subtribe as a whole. Cosmopsaltriina occur in Sulawesi, the Moluccas, New Guinea, Cape York, the Solomon Islands, Vanuatu, Fiji, Tonga and Samoa. The subtribe demonstrates a high rate of endemism on genus, species group and species level. The taxon-area and consensus-area cladograms resulting from Brooks parsimony analysis are discussed in relation to the palaeogeography of the area.     

Homology, biogeography and areas of endemism

Hypotheses of biogeographic homology constitute the basis of historical biogeography. Primary biogeographic homology refers to a conjecture on a common biogeographic history, and secondary biogeographic homology refers to the cladistic test of the formerly recognized homology. Panbiogeography deals with the former, through the recognition of generalized tracks and areas of endemism, whereas cladistic biogeography deals with the latter, through the generation of general area cladograms. A historical biogeographic analysis may include both approaches, in a two‐stage analysis.     

CLADISTIC AND BIOGEOGRAPHIC ANALYSES OF THE WEEVIL GENUS LISTRODERES SCHOENHERR (COLEOPTERA: CURCULIONIDAE)

Abstract— The weevil genus Listroderes Schoenherr is a monophyletic group defined by the body vestiture consisting of subcircular to suboval scales, and comprises 35 species endemic to southern South America. A cladistic analysis of the genus was carried out using 44 characters from external morphology, body vestiture, and male and female genitalia. The curvipes (three species), nodifer (five species) and robustus (four species) species groups and the 23 species of the costirostris species group were considered terminal taxa. Apomorphic states were identified using the genus Hyperoides Marshall as outgroup. The analysis yielded 122 equally parsimonious cladograms, each with 89 steps and a consistency index of 0.42; a successive weighting procedure resulted in nine cladograms (consistency index of 0.69 and retention index of 0.85). In the general consensus cladogram, nodifer-robustus and curvipes-costirostris are two pairs of sister species groups. The costirostris group comprises the subgroups foveatus, angusticeps, costirostris, delaiguei, bimaculatus and elegans , in phylogenetic order. A distributional analysis of the species of Listroderes led to identification of four areas of endemism, namely central Chile, sub-Antarctic, central Argentina and Chaco. A vicariance biogeographic analysis of these areas, based on area cladograms of Listroderes, Hyperoides, Naupactus taeniatulus species group (Coleoptera: Curculionidae), and Lucilia generic group (Asteraceae) was carried out applying the three-area statements technique. According to the general area cladogram the sequence of area-fragmentation is as follows: (central Chile (sub-Antarctic (central Argentina, Chaco))). This sequence is congruent with the history hypothesized for the region, where the uplift of the Andes (Oligocene-Pliocene) led to a progressive aridification, replacing the ancient subtropical forest by open-country environments.     

Cladistic biogeography of the Mexican transition zone

Biogeographic relationships among nine montane areas of endemism across the transition zone between North and South America are analysed cladistically based on phylogenetic hypotheses of thirty‐three resident monophyletic taxa of insects, fish, reptiles, and plants. Areas of endemism include the Arizona mountains (AZ), Sonoran Desert (SD), Sierra Madre Occidental (OCC), southern Sierra Madre Occidental (SOC), Sierra Madre Oriental (ORI), Sierra Transvolcanica (TRAN), Sierra Madre del Sur (SUR), Chiapan‐Guatemalan Highlands (CGH), and Talamancan Cordillera (TC). Area relationships are summarized using Brooks Parsimony Analysis and Assumption 0, with the former resulting in more defensible biogeographic hypotheses. Areas of endemism are dividable into two monophyletic groups; a northern group including AZ, SD, OCC, and ORI, and a southern group consisting of TC, CGH, TRAN, SUR, and the isolated southern regions of the Sierra Madre Occidental (SOC). The northern set of areas are characterized by recent, probably Pleistocene, isolation and prevalent widespread species, whereas the southerly areas probably diverged after Pliocene closure of the Panamanian isthmus. The southern areas are redundantly represented on many of the taxon‐area cladograms by endemic species, indicative of much higher levels of endemism in the Sierra Transvolcanica and further south. Use of a general area cladogram in such a transition zone permits explicit exploration of biogeographic patterns and establishes a predictive framework for taxonomy and conservation prioritization.     

CLADISTIC AND BIOGEOGRAPHIC ANALYSIS OF THE "BLUE ASH' EUCALYPTS

Abstract— A cladistic analysis of the "blue ash" eucalypts ( Eucalyptus , Myrtaceae) is presented. Five equally parsimonious trees were found, and a strict consensus tree constructed. A revised informal classification, recognizing five series ( Planchonianinae, Sphaerocarpinae, Piperitinae, Fraxininae and Haemastominae , informal subgenus Monocalyptus ) is based on the consensus cladogram. A biogeographic analysis applies a new implementation of Assumptions 0 and 1, coding data in the form of three-area statements and using parsimony analysis. These results are used to evaluate hand resolution of Assumption 2. In comparison, Brooks parsimony analysis did not produce area cladograms that best fit the data. Series and subseries were analysed separately for area relationships, which showed a repeated pattern across the blue ash clade; combining all the data in one analysis was seen as equivalent to confounding paralogy and orthology in molecular studies. A resolved area cladogram is presented for southeastern Australia.     

Historical biogeography of Southeast Asia and the West Pacific,or the generality of unrooted area networks as historical biogeographic hypotheses

Aim Unrooted area networks are perhaps a general way in which different historical biogeographical patterns may be combined. Location Southeast Asia up to the West Pacific, Australia, South America. Methods Unrooted area networks based on Primary Brooks Parsimony Analysis of different data sets of Southeast Asian–West Pacific, Australian and South American clades. Results A large Brooks Parsimony historical (cladistic) biogeographic analysis of Southeast Asia and the West Pacific gave a meaningful result when all clades (representing different historical biogeographic patterns) were united into one matrix and an unrooted area network was produced. This network showed geographically adjacent areas as neighbours, which is interpreted as clades dispersing and speciating as soon as areas rafted towards each other. This pseudo‐vicariance mechanism, together with the very limited, mainly linear dispersal possibilities, a few large, widespread clades with many endemic species, and the large overlap in distributions displayed by different patterns, may explain the peculiar result. When applied to examples from other areas (bird data from Australia and South America), unrooted area networks for all data perform very poorly. Main conclusions Unrooted historical general area networks are not universally applicable. In general, it is better to split historical patterns a priori and analyse them separately.     

Biogeographic patterns and the evolution of eureptantic nemerteans

The origin and evolution of the eureptantic nemerteans is discussed from a biogeographic point of view. It is most likely that East Indian Ocean was part of the ancestral distribution of the Eureptantia. The area cladogram estimated by Brooks parsimony analysis (BPA) is to a high degree congruent with a vicariance explanation of the evolution of the Eureptantia and suggests an ancestral distribution concordant with the Tethys Sea. A general area cladogram based on a combined BPA analysis of eureptantic nemerteans and acanthuroid fishes is reconstructed and suggested as a hypothesis of the relationships between east Indian Ocean, west Indian Ocean, west Pacific Ocean, east Adantic Ocean, west Atlantic Ocean, and the Mediterranean. This tree is compared with cladograms from the same areas based on other taxa.     

Possible sister groups and phylogenetic relationships among selected North Pacific and North Atlantic Rhodophyta

Although the cool temperate (boreal) waters of the N. Pacific and N. Atlantic share many similar if not identical species, there have been few studies to test the identity of these species pairs. Whereas such tests are important from a taxonomic perspective, they tell us little if anything about biogeographic relationships. A more useful approach is one employing phylogenetic systematics (cladistics). The interpretation of phylogenetic diagrams (cladograms) in terms of biogeographic area relationships is explained. It is argued that cladistic analyses of taxa occurring in the cool temperate waters of the northern oceans can provide biogeographic tracks, which in turn can suggest the origins and migrations of species and possibly even floras. A number of cool temperate taxa that appear particularly amenable to this approach are discussed, including genera in the Palmariaceae, Corallinaceae, Dumontiaceae, Solieriaceae, Petrocelidaceae, Ceramiaceae and Rhodomelaceae.     

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.     

Biogeographic area relationships of lowland Neotropical rainforest based on raw distributions of vertebrate groups

Hypotheses of the historic biogeography of Neotropical anurans inhabiting lowland forests were generated using Parsimony Analysis of Endemicity. In order to establish comparisons with the biogeographical patterns of other vertebrates, previous cladistic analyses reported in the literature (for lizards and primates) were extended and reanalysed to match the geographical scope of the anuran analysis. Cladistic analysis of the distribution of 335 anuran species at 14 localities showed two regions that form a basal dichotomy: (1) Central America + Choco and (2) Amazon Basin + Brazilian Atlantic Forest. This result is interpreted as the first vicariance event that separated lowland Neotropical rainforests into Cis-Andean (east from the Andes) and Trans-Andean (west from the Andes) areas. Within the Cis-Andean localities, the earliest separation occurred between the Amazon Basin and the Brazilian Atlantic Forest. Within the Amazon Basin, three distinctive clusters are defined: (1) Belem, (2) Guianan Region, and (3) Upper Amazon Basin. Data sets on the distribution of anurans, lizards, and mammals have strong cladistic signal. Strong congruence exists among the area cladograms of anurans, lizards, and primates. All of them have, or at least did not conflict with: (1) a basal separation between Cis- and Trans-Andean regions, (2) a Central American clade, (3) the Choco Region is sister to the Central American clade, (4) an Amazon Basin clade, (5) an Upper Amazon Basin clade, and (6) a Guianan clade. The area cladograms are dichotomous and therefore do not support biogeographic theories that hypothesize simultaneous isolations of biotas in the Neotropics.     

HISTORICAL BIOGEOGRAPHY OF THE HOLARCTIC: AREA RELATIONSHIPS, ANCESTRAL AREAS, AND DISPERSAL OF NON-MARINE ANIMALS

Abstract — Based on published phylogenies for 73 groups of Holarctic non-marine animals, interrelationships between the four Holarctic infraregions (western and eastern Nearctic, western and eastern Palearctic) are examined. The study includes analysis of resolved area cladograms, ancestral areas and dispersal indicated by cladistic subordinateness. Area relationships reflecting present continental configurations (Nearctic vs. Palearctic) dominate the material to the extent that one might speak of a general Holarctic area pattern. Paleocontinental (western Nearctic+eastern Palearctic, western Palearctic+eastern Nearctic) and disjunct patterns are relatively more frequent among groups of higher taxonomic rank. The western Nearctic seems to have played a bigger role than the other infraregions as a center of origin. Two computer programs for constructing resolved area cladograms, viz., COMPONENT 1.5 and COMPONENT 2.0, are compared. The three standard assumptions for biogeographical analysis are compared and arguments are presented in favour of Assumption 0.     

When simplicity is not parsimonious: a priori and a posteriori methods in historical biogeography

Despite using the same null hypothesis, a priori and a posteriori approaches in historical biogeography differ fundamentally. Methods such as Component Analysis (CA) and Reconciled Tree Analysis (RTA) may eliminate or modify input data in order to maximize fit to the null hypothesis, by invoking assumptions 1 and 2. Methods such as Brooks Parsimony Analysis (BPA) modify the null hypothesis, if necessary, to maintain the integrity of the input data, as required by assumption 0. Two exemplars illustrate critical empirical differences between CA/RTA and BPA: (1) CA rather than BPA may select the incorrect general area cladogram for a set of data (2) BPA, not RTA, provides the most parsimonious interpretation of all available data and (3) secondary BPA, proposed in 1990, applied to data sets for which dispersal producing areas with reticulate histories is most parsimonious, provides biologically realistic interpretations of area cladograms. These observations lead to the conclusion that BPA and CA/RTA are designed to implement different research programmes based on different conceptual frameworks. BPA is designed to assess the biogeographic context of speciation events, whereas CA/RTA are designed to find the best fitting pattern of relationships among areas based on the taxa that inhabit them. Unique distributional elements and reticulate (hybrid) histories of areas are essential for explaining complex histories of speciation. The conceptual framework for BPA, thus, assumes biogeographical complexity, relying on parsimony as an explanatory tool to summarize complex results, whereas CA/RTA assumes biogeographical simplicity, assuming conceptual parsimony a priori .     

Application of parsimony analysis of endemicity in Amazonian biogeography: an example with primates

The distributions of 51 non-human primate species are used for Parsimony Analysis of Endemicity (PAE) to determine the relationships among 14 interfluvial regions in the Amazon basin, South America. Two most parsimonious cladograms were found. The strict consensus tree of these cladograms suggests an early separation between Lower Amazonia (eastern) and Upper Amazonia (western). The major clusters of interfluvial regions identified in the PAE cladogram are congruent with the areas of endemism delimited for birds. When interfluvial regions are converted into avian areas of endemism, the PAE cladogram is congruent with one of the two general areas cladograms suggested for Amazonia based on phylogenies of several clades of forest birds. Our analysis suggests that PAE can be used as a tool to objectively identify areas of endemism at an intra-continental scale as well as to make historical inferences. However, the value of a PAE cladogram in this latter application should be always evaluated by congruence with area cladograms built upon cladistic biogeography procedures.     

Revision of the genus Xylomoia Staudinger (Lepidoptera: Noctuidae), with descriptions of two new species

Seven species are included in the genus Xylomoia Staudinger, two of which are new: X. retinax sp.n. from the Novosibirsk area, Western Siberia, and from the Chelyabinsk area, southern Ural Mountains, and X. stangelmaieri sp.n. from Caorle, Venezia Giulia, on the Adriatic coast. A North American species, Chortodes didonea (Smith) comb.n., is removed from the genus. According to a cladistic analysis, the genus Xylomoia comprises one plesiomorphic species group, the chagnoni group, and two apomorphic groups: the graminea and strix groups. The latter are exclusively temperate Palaearctic. Xylomoia chagnoni (Barnes & McDunnough) is the only Nearctic species of the genus, and the loosely related X. apameaoides (Hacker) was recently described from Turkey. In geographical isolation, these two species have retained many ancestral features. In the more central area, the common ancestor of the graminea and strix groups has evolved into at least five species. The locality and rarity of the species of Xylomoia seemingly result from adaptation of the species to moist habitats, the larvae probably bore inside grass stems (the case of X. chagnoni ). What are called lock-and-key mechanisms may lead to the use of non-independent character states in a cladistic analysis; particularly in the case of homoplasy this kind of double-weighting may result in erroneous cladograms. In Xylomoia , deleting female lock-and-keys affected only the number of cladograms produced, whereas omitting the corresponding male characters had profound effects on the cladogram.     

Biogeography of the Lizard Genus Tropidurus Wied-Neuwied, 1825 (Squamata: Tropiduridae): Distribution,Endemism, and Area Relationships in South America

Based on comprehensive distributional records of the 23 species currently assigned to the lizard genus Tropidurus, we investigated patterns of endemism and area relationships in South America. Two biogeographic methods were applied, Parsimony Analysis of Endemicity (PAE) and Brooks Parsimony Analysis (BPA). Two areas of endemism were detected by PAE: the first within the domains of the semiarid Brazilian Caatinga, which includes seven endemic species, and the second in the region of the Serranía de Huanchaca, eastern Bolivia, in which three endemic species are present. The area cladograms recovered a close relationship between the Atlantic Forest and areas of the South American open corridor. The results revealed a close relationship among the provinces Caatinga (Cerrado, Parana Forest (Pantanal+Chaco)). The uplift of the Brazilian Central Plateau in the Late Pliocene-Early Pleistocene (4-2 Myr BP) has been interpreted as a major event responsible for isolation and differentiation of biotas along these areas. However, we emphasize that without the establishment of a temporal framework concerning the diversification history of Tropidurus it is premature to correlate cladogenetic events with specific time periods or putative vicariant scenarios. The limiting factors hampering the understanding of the biogeographic history of this genus include (1) the absence of temporal references in relation to the diversification of distinct clades within Tropidurus; (2) the lack of an appropriate taxonomic resolution of the species complexes currently represented by widely distributed forms; and (3) the need for a comprehensive phylogenetic hypothesis. We suggest that these three important aspects should be prioritized in future investigations.