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.     

Biogeographic area relationships in southern New Zealand: a cladistic analysis of Lepidoptera distributions

ABSTRACT. Recently, attention has been directed toward the application of cladistic techniques to reconstruct the history of areas from species distribution data. In this study, hypotheses of area relationships for southern New Zealand are generated from lepidopteran distribution data analysed at two taxonomic levels. Data are shown to possess cladistic structure and area relationships presented here are consistent with the geological history of the southern region of New Zealand. Our results suggest a recolonization of inland lowland regions from the south following a period of extinction during the early Pliocene. Analysis of selected data including only flightless or locally endemic species resulted in little resolution of area relationships but topologies were significantly congruent with a total species dataset. Hypotheses generated from this study are open to testing with congruence analysis using independent species phylogenies.     

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 biogeographical patterns of the species of Bursera (Burseraceae) and their taxonomic implications

Aim The plant genus Bursera, with 104 species of trees and shrubs, has been used as a model for biogeographical analyses because of its high species richness and large number of endemic species. The biogeographical patterns of Bursera and their implications for its phylogenetic classification are reviewed in order that some hypotheses on the historical biogeography of tropical Mexico can be proposed. Location Bursera is found in the south‐western USA, most of Mexico, mainly below 1700 m elevation in tropical forests, with some species in xeric shrublands, diversifying along the Pacific slope, Central America, and north‐western South America. A few species occur on the Galapagos and Revillagigedo archipelagos, some of which are endemics, whereas in the Antilles species are distributed extensively, with several endemics in the Bahamas, Cuba, Jamaica, and Hispaniola. Methods Data from specimens in herbaria and the literature were used to construct a matrix of 104 species in 160 areas. Distributional patterns of the species of Bursera were inferred applying track analysis, parsimony analysis of endemicity (PAE), and Brooks parsimony analysis (BPA). Results Track analysis revealed four individual tracks: (1) a circum‐Caribbean track, comprising species of the Bursera simaruba species group; (2) an Antillean track, including species that have been transferred to Commiphora based on their pollen traits; (3) a Mexican Pacific track, including species of the B. fragilis, B. microphylla, and B. fagaroides species groups, called ‘cuajiotes’; and (4) a Neotropical Pacific track, including the two species groups assigned to section Bullockia, in which the individual track of the Bursera copallifera species group is nested within the track of the B. glabrifolia species group. The four tracks overlap in a node in the Mexican Pacific slope, where they are highly diversified. PAE allowed us to identify 22 areas of endemism: 12 in Mexico (11 along the Mexican Pacific slope), six in the Antilles, two in Central America, one in South America, and one in the Galapagos. The general area cladogram obtained by BPA has two main clades: one includes the greater Antilles; and the other, 12 Mexican areas of endemism. Main conclusions Bursera fragilis, B. microphylla, and B. fagaroides species groups can be treated together as a new section within Bursera, sect. Quaxiotea, because they are segregated from the other groups of sect. Bursera based on morphological, anatomical, molecular and geographical evidence.     

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.     

Areas of endemism and distribution patterns for Neotropical Piper species (Piperaceae)

Aim The study aimed to establish areas of endemism and distribution patterns for Neotropical species of the genus Piper in the Neotropical and Andean regions by means of parsimony analysis of endemicity (PAE) and track‐compatibility analysis. Location The study area includes the Neotropical region and the Northern Andean region (Páramo‐Punan subregion). Methods We used distribution information from herbarium specimens and recent monographic revisions for 1152 species of Piper from the Neotropics. First, a PAE was attempted in order to delimit the areas of endemism. Second, we performed a track‐compatibility analysis to establish distribution patterns for Neotropical species of Piper. Terminology for grouping Piper is based on recent phylogenetic analyses. Results The PAE yielded 104 small endemic areas for the genus Piper, 80 of which are in the Caribbean, Amazonian and Paranensis subregions of the Neotropical region, and 24 in the Páramo‐Punan subregion of the Andean region. Track‐compatibility analysis revealed 26 generalized tracks, one in the Páramo‐Punan subregion (Andean region), 19 in the Neotropical region, and six connecting the Andean and Neotropical regions. Both the generalized tracks and endemic areas indicate that distribution of Piper species is restricted to forest areas in the Andes, Amazonia, Chocó, Central America, the Guayana Shield and the Brazilian Atlantic coast. Main conclusions Piper should not be considered an Andean‐centred group as it represents two large species components with distributions centred in the Amazonian and Andean regions. Furthermore, areas of greater species richness and/or endemism are restricted to lowland habitats belonging to the Neotropical region. The distribution patterns of Neotropical species of Piper could be explained by recent events in the Neotropical region, as is the case for the track connecting Chocó and Central America, where most of the species rich groups of the genus are found. Two kinds of event could explain the biogeography of a large part of the Piper taxa with Andean–Amazonian distribution: pre‐Andean and post‐Andean events.     

Distribution patterns of the genus Pacifigorgia (Octocorallia: Gorgoniidae): track compatibility analysis and parsimony analysis of endemicity

Aim We analysed the distribution patterns of the eastern Pacific octocoral genus Pacifigorgia and deduced its ancestral distribution to determine why Pacifigorgia is absent from the Gulf of Mexico, the Caribbean of central America, and the Antilles. We also examined the current patterns of endemism for Pacifigorgia to look for congruence between hot spots of endemism in the genus and generally recognized areas of endemism for the eastern Pacific. Location The tropical eastern Pacific and western Atlantic, America. Methods We used track compatibility analysis (TCA) and parsimony analysis of endemicity (PAE) to derive ancestral distribution patterns and hot spots of endemism, respectively. Distributional data for Pacifigorgia were gathered from several museum collections and from fieldwork, particularly in the Pacific of Costa Rica and Panama. Results A single generalized track joined the three main continental eastern Pacific biogeographical provinces and the western Atlantic. This track can be included within a larger eastern Atlantic–eastern Pacific transoceanic track that may be the oldest transoceanic track occurring in the region. PAE results designate previously recognized eastern Pacific biogeographical provinces as Pacifigorgia hot spots of endemism. The number of endemic species, which for other taxonomic groups is similar among the eastern Pacific provinces, is higher in the Panamic province for Pacifigorgia. Main conclusions We propose that the absence of Pacifigorgia from the Gulf of Mexico, the Caribbean of central America, and the Antilles is the result of an ancient absence of the genus from these areas rather than the consequence of a major, recent, extinction episode. The Cortez province and the Mexican province appear together as a result of either non‐response to vicariance or dispersal across the Sinaloan Gap. We posit that the Central American Gap acts as a barrier that separates the Panamic province from the northern Cortez–Mexican province.     

Cladistic analysis of distributions and endemism (CADE): using raw distributions of birds to unravel the biogeography of the South American aridlands

Aim To use published distributional and taxonomic information on Neotropical birds in a cladistic analysis of distributions and endemism (CADE) to generate a testable hypothesis of area‐relationships for the arid areas of endemism, particularly those of Central South America (the ‘arid diagonal’), and to clarify the different methodologies commonly associated with parsimony analysis of endemicity (PAE). Location South America. Methods Cladistic analysis of distributions and endemism. Results We obtain a tree where the relationships of most areas are resolved, and we find support for an exclusive clade of Central South American areas, with the Caatinga as sister to both the Chaco and Cerrado. Main conclusions There is a substantial amount of historical signal in avian distributions, when large numbers of taxa and multiple taxonomic levels are considered. Ecological noise and historical information are more easily distinguished in CADE analyses than they would be in PAE analyses. Based on our results we predict that among aridland birds, the Cerrado and Chaco species will be more closely related to each other than to Caatinga species.     

Biogeographic regions of North American mammals based on endemism

Since the 19th Century, two regions have been recognized for North American mammals, which overlap in Mexico. The Nearctic region corresponds to the northern areas and the Neotropical region corresponds to the southern ones. There are no recent regionalizations for these regions under the criterion of endemism. In the present study, we integrate two methods to regionalize North America, using species distribution models of mammals: endemicity analysis (EA) and parsimony analysis of endemicity (PAE). EA was used to obtain areas of endemism and PAE was used to hierarchize them. We found 76 consensus areas from 329 sets classified in 146 cladograms, and the strict consensus cladogram shows a basal polytomy with 14 areas and 16 clades. The final regionalization recognizes two regions (Nearctic and Neotropical) and a transition zone (Mexican Transition Zone), six subregions (Canadian, Alleghanian, Californian‐Rocky Mountain, Pacific Central America, Mexican Gulf‐Central America, and Central America), two dominions (Californian and Rocky Mountain), and 23 provinces. Our analysis show that North America is probably more complex than previously assumed. © 2013 The Linnean Society of London, Biological Journal of the Linnean Society, 2013, 110 , 485–499.     

Phylogenetic relationships among genera of danaine butterflies (Lepidoptera: Nymphalidae) as implied by morphology and DNA sequences

Cladistic relationships among genera and subtribes of Danaini (the milkweed butterflies) were inferred by analysis of data combined from five sources: morphology of adults and immature stages, and DNA sequences from three gene regions. The results corroborate and greatly increase support for prior hypotheses based on morphology alone. A new index summarizing incongruence among data partitions, the Partition Congruence Proportion (PCP), is introduced. The significance of the inferred pattern of phylogenetic relationships for comparative chemical ecology of milkweed butterflies is briefly discussed.     

Phylogeographic patterns of trans-Amazonian vicariants and Amazonian biogeography: the Neotropical rattlesnake (Crotalus durissus complex) as an example

Aim To investigate the phylogeography and execute a historical‐demographic analysis of the Neotropical rattlesnake, Crotalus durissus, thereby testing the hypothesis of a Pleistocene central Amazon corridor of dry forest or savanna that partitioned the Amazonian rain forest into western and eastern portions. Location South America. Methods Using sequences of three mitochondrial genes, we estimated the phylogeography, gene and nucleotide diversity across the South American range of C. durissus. Tree topology tests were used to test alternative biogeographical hypotheses, and tests of population genetic structure and statistical parsimony networks and nested clade phylogeographic analysis (NCPA) were used to infer connectivity and historical population processes on both sides of the Amazon basin. Results Tree topology tests rejected the hypothesis of a coastal dispersal in favour of a central corridor scenario. Gene diversity was similar on both sides of the Amazon basin. Nucleotide diversity indicated that the populations from north of the Amazon basin represented ancestral populations. Analysis of molecular variance (amova ) showed that intra‐population molecular variation was greater than between regions. Historical‐demographic statistics showed significant population expansion south of the Amazon, and little differentiation in the north, indicating moderate past gene flow between north and south of the Amazon. The parsimony network connected clades from the Roraima and Guyana populations with Mato Grosso, suggesting an Amazonian central corridor, and NCPA supported allopatric fragmentation between north and south of the Amazon. Main conclusions The distribution of C. durissus on both sides of the Amazon basin is evidence of changes in the distribution of rain forest vegetation during the Pleistocene. Our results suggest a formerly continuous distribution of this rattlesnake along a central Amazonian corridor during the middle Pleistocene. Allopatric fragmentation inferred from NCPA is consistent with vicariance resulting from a subsequent closure of this habitat corridor. This study emphasizes the potential of trans‐Amazonian open formation species to inform the debate on the past distribution of rain forests in the Amazon Basin.     

Patterns of species richness and biogeographic regionalization of the avifaunas of the seasonally dry tropical forest in Mesoamerica

Biogeographic patterns of avifaunas associated with seasonally dry tropical forests in Mesoamerica are poorly understood despite their high levels of species richness and endemism. Through the parsimony analysis of endemicity, we analyzed biogeographic relationships of 650 resident species of birds associated with seasonally dry tropical forests from Mexico to Panama, based on potential distributions obtained through ecological niche modeling. Results show two general avifaunal groups, east and west of the Isthmus of Tehuantepec. Patterns of biogeographic distribution and species richness also helped illuminate the importance of key areas for birds associated to this habitat in the region.

Los patrones biogeográficos de las avifaunas asociadas a los bosques tropicales estacionalmente secos en Mesoamérica están pobremente entendidos, a pesar de que estas áreas poseen una gran riqueza de especies y endemismo. Analizamos las relaciones biogeográficas con base en distribuciones potenciales, hechas a partir de modelos del nicho ecológico usando el análisis de parsimonia de endemismos, de 650 especies de aves residentes asociadas a los bosques tropicales estacionalmente secos desde México hasta Panamá. Los resultados muestran dos grupos generales de la avifauna, al este y oeste del Istmo de Tehuantepec. El contexto biogeográfico y la riqueza de especies resalta también la importancia de áreas clave para las aves asociadas a este tipo de hábitat en la región.     

Area-relationships in the Neotropical lowlands: an hypothesis based on raw distributions of Passerine birds

Abstract. Using raw geographic distributions for Neotropical species and subspecies of the perching birds (Order Passeriformes), we present an hypothesis of area-relationships for twelve avian areas of endemism in the lowland Neotropics. With 1717 characters (distributions of species and subspecies) we find a single most parsimonious tree of area-relationships. This topology does not match area-relationships determined from phylogenetic studies of morphologic characters in some Neotropical birds. Analyses of data partitions representing major taxonomic subdivisions within Passerine birds provide many different hypotheses of area-relationships. These results suggest that a single set of Neotropical area-relationships is not likely. In the future, we suggest greater emphasis be placed on research to document patterns in the Neotropics, particularly phylogenetic patterns, than on speculation about what processes have been important for diversification.     

Critique of parsimony analysis of endemicity as a method of historical biogeography

Aim Assess the value of parsimony analysis of endemism as either an a priori (cladistic) and an a posteriori (phylogenetic) method of historical biogeography. Location World‐wide. Methods Parsimony analysis of endemicity (PAE) and Brooks parsimony analysis (BPA). Results Parsimony analysis of endemicity is capable of finding correct and unambiguous area relationships only under scenarios of vicariance in combination with non‐response to vicariance or extinction. An empirical comparison between PAE and BPA, using the poeciliid fish genera Heterandria and Xiphophorus, demonstrates that PAE fails to document much of the historical complexity in this relatively simple system. Main conclusions The a priori assumptions of PAE are far more restrictive than those made by other a priori methods, limiting its utility as a method of cladistic biogeography. The inability of PAE to detect perfect vicariance or biogeographical histories involving dispersal, renders it unsuitable as a method of phylogenetic biogeography.     

Biogeographic history of geminate cirrhitoids (Perciformes: Cirrhitoidea) with east–west allopatric distributions across southern Australia, based on molecular data

The biogeographic history of three cirrhitoid species pairs with east–west allopatric distributions across southern Australia was examined by determining levels of mitochondrial DNA sequence divergence and applying molecular clock calibrations. Similar levels of genetic divergence were observed for Aplodactylus Valenciennes and Goniistius Gill species pairs, but these were more than twice that observed for a Nemadactylus Richardson pair. Molecular clock calibrations suggested divergences occurred during the late Miocene and mid Pliocene, respectively. Given evidence of high dispersal capabilities, the habitat and climatic barriers of the Australian south coast appear too small to have facilitated speciation of the cirrhitoids examined. A mechanism is proposed by which ancestral cirrhitoids were vicariantly isolated into east and west coast populations during periods of climate change. Although Aplodactylus and Goniistius divergences occurred during the same period, separate vicariant events across the Australian north and south coasts are invoked.     

Time and space in biogeography: response to Parenti & Ebach (2013)

A recent Guest Editorial by Parenti & Ebach (2013, Journal of Biogeography, 40, 813–820) disagrees with the methods or interpretations in two of our recent papers. In addition, the authors open a debate on biogeographical concepts, and present an alternative philosophy for biogeographical research in the context of their recently described biogeographical subregion called ‘Pandora’. We disagree with their approach and conclusions, and comment on several issues related to our differing conceptual approaches for biogeographical research; namely, our use of molecular phylogenetic analyses, including time estimates; and Parenti & Ebach's reliance on taxon/general area cladograms. Finally, we re‐examine their ‘tests’ supporting the existence of ‘Pandora’.     

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.