SYSTEMATICS AND BIOGEOGRAPHY OF THE AUSTRALIAN "GREEN ASH" EUCALYPTS (MONOCALYPTUS)

Abstract— A cladistic analysis of the "green ash" eucalypts, informal subgenus " Monocalyptus ", is presented- As a first step, ordination methods of principal coordinates analysis and multidimensional scaling delineated some terminal taxa. The cladistic analysis, applying parsimony methods to the unweighted data set, yielded 25 equally parsimonious trees, each with a consistency index of 0.57.
Farris' successive approximations approach to character weighting produced one tree with a consistency index of 0.74.
An informal classification of the group, superseries Eucalyptus , is based on that cladogram. The biogeographic history of superseries Eucalyptus is interpreted from the cladogram as having been caused by lour vicariant events in southeastern Australia, in combination with a suite of ecological features that overlie the biogeographic area-pattern.     

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.     

Marine Area Relationships from Twenty Sponge Phylogenies. A Comparison of Methods and Coding Strategies

Published phylogenies of 20 marine sponge groups are used to build general area cladograms of marine areas of endemism under three different methods for which algorithms adapted for personal computers are available, viz. COMPONENT, BPA and TAS, and two different coding strategies, Assumption 0 (A0) and "no assumption" (NA). The latter is a recently proposed procedure for handling the distributions of widespread taxa by treating these as separate areas of endemism, rather than as suites of smaller constituent areas. The 20 phylogenies contained large numbers of problem data which prevented an exhaustive search for all possible equally "best" general area cladograms. The Nelson consensus trees and their equivalents in parsimony analysis for all six attempts (viz. three different methodologies under two different coding strategies) were compared using their fit with the 20 sponge phylogenies as a measure of quality. Fit was determined using the number of "cospeciations" between a general area cladogram and a taxon area cladogram computed with TreeMap 1.0. No single method or coding strategy yielded a clearly better fit, each cladogram fitting variously better or worse with various phylogenies. In general, fit with NA coding was higher than with A0 coding, but random tree tests failed to generate statistically significant support for the conclusion that NA coding improves fit. Assuming that available sponge phylogenies are representative of marine benthic groups, software and hardware limitations are serious obstacles to a successful development of marine general area cladograms under any method or coding strategy.     

Regionalization of the avifauna of the Baja California Peninsula, Mexico: a parsimony analysis of endemicity and distributional modelling approach

Aim To analyse the distributional patterns of the Baja California Peninsula's resident avifauna, and to generate a regionalization based on a method that uses a parsimony analysis (parsimony analysis of endemicity, PAE) of point data and modelled potential distributions. Location The Baja California Peninsula, Mexico. Methods A data base was constructed containing records of 113 species of resident terrestrial birds present in the Baja California Peninsula. Records and localities were obtained from the literature and from specimens housed in scientific collections world‐wide. Raw data points and potential distribution maps obtained using the software Genetic Algorithms for Rule‐set Prediction (GARP), were analysed with PAE. Results The data base consisted of 4164 unique records (only one combination of species/locality) belonging to 113 terrestrial resident bird species, in a total of 809 localities. From the point distribution matrix, the analysis generated 500 equally parsimonious trees, from which a strict consensus cladogram with 967 steps was obtained. The cladogram shows a basal polytomy and some geographical correspondence of a few resolved groups obtained in the analysis. These results do not allow the recognition of areas defined by avifaunistic associations. From the potential distribution matrix, the analysis generated 501 equally parsimonious trees, and a strict consensus cladogram of 516 steps was obtained. The cladogram shows a higher resolution because of the number of resolved groups with better geographical correspondence and therefore regions are well‐defined. Main conclusions The correspondence of some groupings of species suggest their validity as areas with biogeographical (historical and/or ecological) meaning. This regionalization in the Baja California avifauna seems to be consistent with previous regionalizations for other groups. Hence, PAE is a useful tool for area categorization if reliable point records and prediction tools are available. Our results suggest that the geographical definition is much better using potential data generated by GARP, particularly when they are contrasted with the results from point data. Thus, this is an excellent alternative for developing biogeographical studies, as well as for improving the use of data from scientific collections and other sources of biodiversity information.     

Parsimony analysis of endemicity (PAE) of Mexican terrestrial mammals at different area units: when size matters

Abstract Aim Parsimony analysis of endemicity (PAE) is a biogeographical method that uses a parsimony algorithm to obtain an area cladogram, based on taxa inhabiting the study areas. We compare its performance at different geographical units (½° and 1° quadrats, ecoregions and biogeographical provinces) to analyse distributional patterns of Mexican terrestrial mammals, in order to assess the importance of the size of area units. Location The area analysed corresponds to Mexico. Methods Parsimony analyses were based on 56,859 collection records, corresponding to 703 genera, species and subspecies. Four data matrices were constructed for: (1) 716 quadrats of ½° latitude × ½° longitude, (2) 230 quadrats of 1° latitude × 1° longitude, (3) forty‐five ecoregions and (4) fourteen biogeographical provinces. Results For the ½° quadrat matrix, we obtained six cladograms of 17,138 steps. For the 1° quadrat matrix, we obtained five cladograms (strict consensus with 9394 steps). For the matrix of ecoregions, we obtained twelve cladograms (strict consensus cladogram with 3009 steps). For the provinces, we obtained a single cladogram with 1603 steps. Main conclusions The best results were obtained with natural areas instead of quadrats. There seems to exist a trend to decrease the absolute number of steps and an increase in the absolute and relative number of synapomorphies as the size of the area units decreases, although this does not necessarily occur for the number of cladograms.     

Historical biogeography of some river basins in central Mexico evidenced by their goodeine freshwater fishes: a preliminary hypothesis using secondary Brooks parsimony analysis

Aims Our aim was to uncover and describe patterns of historical biogeography of the main river basins in central Mexico, based on a secondary Brooks parsimony analysis (BPA) of goodeine fishes, and to understand the processes that determine them with respect to the molecular clock of the goodeines and the geological events that have taken place in the region since the Miocene. Location The region covered in this study includes central Mexico, mostly the so‐called Mesa Central of Mexico, an area argued to be a transitional zone comprising several major river drainages from their headwaters at high elevations along the Transmexican Volcanic Belt to the coast of the Gulf of Mexico and the Pacific Ocean. Methods Based on a previous phylogenetic hypothesis regarding the Goodeidae, we built a data matrix using additive binary coding. First, we conducted a primary BPA to provide general explanations of the historical biogeography of Central Mexico. As ambiguity was found, a secondary BPA was conducted, and some areas were duplicated in order to explain the reticulated history of the area. Area cladograms were obtained by running a parsimony analysis. Instances of vicariance and non‐vicariance processes were described with reference to the cladogram obtained from secondary BPA. Results The study area was divided into 18 discrete regions. Primary BPA produced nine equally parsimonious cladograms with 129 steps, and a consistency index (CI) of 0.574. A strict consensus cladogram shows low resolution among some areas, but other area relationships are consistent. For secondary BPA, five of the 18 regions were duplicated (LEA, COT, AYU, CUT, PAN); one was triplicated (BAL); and one was quadruplicated (AME), suggesting that the pattern of distribution of species in these areas reflects multiple independent events. These areas correspond with the regions exhibiting the highest levels of diversification and the most complex geological history, and those for which river piracy events or basin connections have been proposed. The secondary BPA produced a single most parsimonious cladogram with 118 steps, and a CI of 0.858. This cladogram shows that none of the duplicated areas are nested together, reinforcing the idea of a reticulated history of the areas and not a single vicariant event. Main conclusions Although our results are preliminary and we cannot establish this as a general pattern, as the BPA is based on a single‐taxon cladogram, resolution obtained in the secondary BPA provides some insights regarding the historical biogeography of this group of fishes in river basins of central Mexico. Secondary BPA indicates that the historical biogeography of central Mexico, as shown by their goodeine freshwater fishes, is complex and is a result of a series of vicariant and non‐vicariant events such as post‐dispersal speciation and post‐speciation dispersal.     

Do the Oaxacan Highlands represent a natural biotic unit? A cladistic biogeographical test based on vertebrate taxa

Aim  We analysed the distributional patterns of six terrestrial vertebrate taxa from the Oaxacan Highlands (Sierra Mazateca, Nudo de Zempoaltépetl and Sierra de Juárez) through a cladistic biogeographical approach, in order to test their naturalness as a biotic unit.
Location  The Oaxacan Highlands, Mexico.
Methods  The cladistic biogeographical analysis was based on the area cladograms of the Pseudoeurycea bellii species group (Amphibia: Plethodontidae), the genus Chlorospingus (Aves: Thraupidae), the genera Microtus , Reithrodontomys and Habromys , and the Peromyscus aztecus species group (Mammalia: Rodentia). We obtained paralogy-free subtrees, from which the components were coded in a data matrix for parsimony analysis. The data matrix was analysed with N ona through W in C lada .
Results  The parsimony analysis resulted in a single general area cladogram in which areas were fragmented following the sequence Sierra Madre Occidental, Trans-Mexican Volcanic Belt, Chiapas, Sierra Madre Oriental + Sierra Mazateca, Sierra Madre del Sur, Nudo de Zempoaltépetl and Sierra de Juárez.
Main conclusions  The general area cladogram shows that the Oaxacan Highlands do not constitute a natural unit. The Sierra Mazateca is the sister area to the Sierra Madre Oriental, whereas the Nudo de Zempoaltépetl and the Sierra de Juárez are closely related to the Sierra Madre del Sur. The events that might have caused these patterns include cycles of expansion and contraction of mountain pinyon, juniper and oak woodlands during the Pleistocene.     

Molecular phylogenetics of the tribeInuleae s. str.(Asteraceae), based on ITS sequences of nuclear ribosomal DNA

The sequences of the internal transcribed spacer (ITS) region of 18S–26S nrDNA for a sample of 16 taxa from theInuleae s. str. and two outgroup taxa are analysed cladistically with PAUP. A consensus tree of the four most parsimonious cladograms is presented. Three different tests of cladogram stability are conducted (Bremer support, parsimony jackknifing and bootstrapping); all tests indicate a high degree of support for the basal nodes of the tree. The ITS phylogeny of the tribe is compared with previous hypotheses based on morphological data. The position ofAnisopappus as sister group to the rest of the tribe is supported by the molecular data, but the proposed subdivision ofInuleae s. str. into a paleate grade group and an epaleate clade is not. The interpretation of the character evolution of, e.g. receptacular paleae and pappus features within the tribe is discussed.     

A CLADISTIC ANALYSIS OF ANGOPHORA CAV. (MYRTACEAE)

Abstract— A cladistie analysis of Angophora Cav. used a data set dominated by quantitative morphological characters. These were coded into multistates using Generalized Gap-Coding, and treated as ordered sequences of stales. The reasons for choosing an ordered over an unordered sequence are discussed. A branch and bound method yielded one minimal-length, unrooted tree. Because of uncertainty in the position of the root, five cladograms were derived from the unrooted tree. The consensus cladogram comprises four main clades. The consensus cladogram was used for a biogeographic study using component analysis, which generated a single statement of relationships for five areas of eastern Australia. An infra-generic classification of Angophora comprising four series corresponding to the four main clades, and two subseries, is presented. The following new names are published: Angophora series i>Floribundinae , series Subvelutininae , series Bakerinae . subseries Costntitac. Angophora leiocarpa : L. Johnson ex G. Leach) K. R. Thiele and P. Y. Ladiges and A.paludosa (G. Leach) K. R. Thiele and P. Y. Ladiges are published as new combinations.     

A Review of Current Theories and Methods in Cladistics and a Cladistic Study of Twelve Lindera Species in Eastern China

Cladistics has become a widely used method for phylogenetic reconstruction．Because of rapid improvement Of cladistic theories and methodologies,and application of new data,especially,molecular data,it is becoming realistic to reconstruct phylogenies of organisms,and to establish natural classifications based on these phylogenies．This paper reviews some current cladistic theories and methods in a practical way,such as choosing characters,defining character states,polarizing characters,analyzing data matrices, calculating consensus cladograms,choosing among multiple equally most parsimonious cladograms,estimating reliability of cladograms,and applying cladograms to classification, character evolution,and biogeography． Based on 36 morphological characters．a parsimony analysis of 12 species representing six sections in subgenus Lindera and an outgroup species from subgenus lteodaphne of the genus Lindera(Lauraceae)was conducted．The results suggest a close relationship between section Lindera and section Sphaerocarpae,which is different from the previous phylogenetic hypothesis within the genus．In the strict consensus cladogram,two species,L．megaphylla and L.chienii,from section Cupuliformes are in the most primitive and the most advanced clades respectively,indicating that the section is polyphyletic．The cladogram also suggests that section Lindera be a polyphyletic group．     

分支系统学当前的理论和方法概述及华东地区山胡椒属十二个种的分支系统学研究

本文概述了当前分支系统学研究中涉及的主要理论和方法,包括性状的选取、性状状态和极性的确定、数据矩阵的分析计算、结果分支图的处理、分支图可靠性的评价及分支图的应用。本文同时以华东地区樟科山胡椒属Linderal2个种的分支系统学研究为例,讨论了用形态性状进行分支系统学研究中可能遇到的问题,也揭示了一些分支系统学与传统的系统学在应用性状推导进化关系上的不同点。对这12个种的分支系统学研究得出了一些不同于传统系统学方法所推测的山胡椒属内的系统发育关系,如分支系统学研究显示山胡椒组和球果组很近缘。在严格一致性分支图上,杯托组的黑壳楠和江浙山胡椒分别位于最原始和最进化的分支,表明这个组是复系类群。分支图也显示山胡椒组可能是复系类群。     

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.     

Systematics of Nothofagus (Nothofagaceae) based on rDNA spacer sequences (ITS): taxonomic congruence with morphology and plastid sequences

Phylogenetic relationships were examined within the southern beech family Nothofagaceae using 22 species representing the four currently recognized subgenera and related outgroups. Nuclear ribosomal DNA sequences encoding the 5.8s rRNA and two flanking internal transcribed spacers (ITS) provided 95 phylogenetically informative nucleotide sites from a single alignment of ~588 bases per species. Parsimony analysis of this variation produced two equally parsimonious trees supporting four monophyletic groups, which correspond to groups designated by pollen type. These topologies were compared to trees from reanalyses of previously reported rbcL sequences and a modified morphological data set. Results from parsimony analysis of the three data sets were highly congruent, with topological differences restricted to the placement of a few terminal taxa. Combined analysis of molecular and morphological data produced six equally parsimonious trees. The consensus of these trees suggests two basal clades within Nothofagus. Within the larger of the two clades, tropical Nothofagus (subgenus Brassospora) of New Guinea and New Caledonia are strongly supported as sister to cool-temperate species of South America (subgenus Nothofagus). Most of the morphological apomorphies of the cupule, fruit, and pollen of Nothofagus are distributed within this larger clade. An area cladogram based on the consensus of combined data supports three trans-Antarctic relationships, two within pollen groups and one between pollen groups. Fossil data support continuous ancestral distributions for all four pollen groups prior to continental drift; therefore, vicariance adequately explains two of these disjunctions. Extinction of trans-Antarctic sister taxa within formerly widespread pollen groups explains the third disjunction; this results in a biogeographic pattern indicative of phylogenetic relationship not vicariance. For the biogeographically informative vicariant clades, area relationships based on total evidence support the recently advanced hypothesis that New Zealand and Australia share a unique common ancestry. Contrary to previous thought, the distribution of extant Nothofagus is informative on the area relationships of the Southern Hemisphere, once precise phylogenetic relationships are placed in the context of fossil data.     

The future of phylogeny reconstruction

A new approach to phylogenetic analysis, parsimony jackknifing, uses simple parsimony calculations combined with resampling of characters to arrive at a tree comprising well-supported groups. This is usually much the same as the consensus of most-parsimonious trees found from extensive multiple-tree calculations, but the new method is thousands of times faster, allowing analysis of much larger data matrices, and also provides information on the strength of support for different groups. Jackknife frequencies provide a more reliable assessment of support than do alternative methods, notably "confidence probability" (CP) and T-PTP testing.     

Phylogeny of Melaleuca, Callistemon, and Related Genera of the Beaufortia Suballiance (Myrtaceae) Based on 5S and ITS-1 Spacer Regions of nrDNA

A phylogenetic analysis of genera within the informal suballiance Beaufortia (family Myrtaceae), largely endemic to Australia and New Caledonia, is presented based on separate and combined data sets for 5S and ITS-1 spacer regions of nuclear ribosomal DNA. The two sets were not in conflict but the 5S data set was more informative. Data were analysed using conventional parsimony, jackknife parsimony, and three-item parsimony analyses. Three-item analysis gave more resolved trees than conventional parsimony analysis. The Beaufortia suballiance includes two major clades, with all Australian representatives of Callistemon (shown to be monophyletic) and most Australian representatives of Melaleuca forming one of these. The sister clade comprises a well-defined group of endemic New Caledonian taxa (classified as Callistemon and Melaleuca ), some Australian species of Melaleuca , a clade including the Western Australia/Northern Territory genera Beaufortia, Lamarchea , and Regelia , and a clade including the south-west Western Australian genera Calothamnus, Eremaea, Conothamnus , and Phymatocarpus . All molecular analyses sup port the monophyly of Conothamnus and of Regelia , genera for which a number of species were included. Three-item analysis of the combined data set supports the monophyly of Beaufortia . The findings have implications for both taxonomy and biogeography.     

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.     

Phylogeny of the subfamilies of Chironomidae (Diptera)

Summary The phylogeny of the subfamilies of Chironomidae are cladistically analysed using parsimony. A data matrix is presented and some characters discussed. Different outgroup taxa, constraints and options are used, characters unordered or ordered, weighted or unweighted, the results reweighted or not and the results discussed. Telmatogetoninae in all cladograms forms the sister group of the remaining subfamilies. Aphroteniinae in some cladograms forms the sister group of all subfamilies except Telmatogetoninae, whereas in other cladograms, including the preferred cladogram, it is part of Tanypodoinae, which otherwise includes Podonominae, Usumbaromyiinae and Tanypodinae. Chilenomyiinae is basal in Tanypodoinae in some cladograms. In most cladograms, including the preferred cladogram, it is basal in Chironomoinae, which also includes Buchonomyiinae, Diamesinae, Prodiamesinae, Orthocladiinae and Chironominae. The preferred cladogram is compared with the relationships between different subfamilies suggested by previous authors.     

Systematics and biogeography of Polietina Schnabl & Dziedzicki (Diptera, Muscidae): Neotropical area relationships and Amazonia as a composite area

Abstract.  The genus Polietina Schnabl & Dziedzicki, 1911 (Diptera, Muscidae) groups 15 species distributed throughout the Neotropical region. Here, generic and specific diagnoses and a species identification key are provided, with cladistic and biogeographical analyses performed and results discussed. In the cladistic analysis, the application of equal, successive and implied character weighting schemes resulted in the single cladogram (( P. flavidicincta ( P. rubella ( P. concinna ( P. orbitalis , P. wulpi )))) ( P. steini (( P. flavithorax , P. major ) ( P. nigra , P. prima ) ( P. bicolor , P. minor , P. univittata )))). In the biogeographical analysis, the Brooks parsimony analysis was performed by experimenting several combinations of areas of endemism proposed previously in the literature, and one area cladogram ((Caribbean, north-west Amazonia) (south-east Amazonia (Chacoan, Paraná))) favours a previously proposed hypothesis of a composite history for Amazonia.