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.     

Biogeographic analysis of endemic cacti of the Sierra Madre Oriental, Mexico

The distribution of cacti species that inhabit the Sierra Madre Oriental (SMO) was analysed. Grid-cells were analysed using parsimony analysis of endemicity (PAE) and endemism indices. Areas characterized by their diagnostic species were determined, aiming to propose areas for the conservation of threatened cacti. Distributional data were obtained from 1936 herbarium specimens, electronic information, and from field collections. Eight areas of endemism and three main clades were obtained from the grid-cell analysis. Areas obtained from the endemism indices are very similar to those obtained with the PAE, but differ in the association of grid-cells. PAE showed endemism patterns indicating that southern and central sections of the SMO province are the areas richest in geographically-restricted species. The results obtained with different endemism indices detected more or less the same areas, although the importance level is different. The corrected weighted endemism index can be considered as a reliable measure of endemism because it is unrelated to species richness. A regionalization of the SMO in three subprovinces is suggested, supported by characteristic cacti taxa and the existence of natural barriers.  © 2009 The Linnean Society of London, Biological Journal of the Linnean Society , 2009, 97 , 373–389.     

Distributional modelling and parsimony analysis of endemicity of Senecio in the Mediterranean-type climate area of Central Chile

Aim Floristic blocks and areas of endemism resulting from a parsimony analysis of endemicity (PAE) using raw floristic data versus data generated from distributional modelling for 130 species in the genus Senecio Tourn. ex L. distributed in the Mediterranean‐type climate area of Central Chile were compared, and the results were used to identify conservation priorities for the flora of the region. Location Central Chile, between 30° and 38° S. Methods Using herbarium records, a species × area matrix consisting of presence/absence data was constructed from a 0.5° × 0.5° grid. Distributional modelling techniques incorporating vegetation formations, elevation and the contagion index were used to interpolate floristic composition of poorly known areas. Parsimony analysis of endemicity was used to identify floristic blocks and areas of endemism. Results Using the number of most parsimonious trees as an index, distributional modelling greatly optimized the results of the PAE analysis. Three floristic blocks and four areas of endemism were suggested based on the PAE results using potential distribution data not incorporating the contagion index, while four blocks and two areas of endemism were suggested from the PAE results using potential distribution data incorporating the contagion index. Floristic blocks for the northern coast, southern Andes, and northern/central Andes were found, with some blocks showing divisions within them representing distinct geographic subunits. Major breaks between and within floristic blocks were identified at 32.5°–33° S and 34.5°–35° S. Main conclusions The floristic blocks identified with the distributional modelling and PAE correspond well to results from some previous studies and support hypothesized biogeographic divisions within Central Chile. The results were similar to those obtained from parallel analysis of the entire tree flora of Central Chile. The vegetative formation‐based distributional modelling produced robust and reproducible results when used along with PAE, especially when the contagion index was incorporated, and is a useful technique for area classification. The results demonstrate the utility of Senecio as an indicator genus for biogeography and conservation in southern South America.     

Application of parsimony analysis of endemicity to Mexican gymnosperm distributions: grid-cells, biogeographical provinces and track analysis

Parsimony analysis of endemicity (PAE) was used to analyse the distributional patterns of 124 species of Mexican gymnosperms, using two different sample units: grid-cells and biogeographical provinces. PAE analyses were based on distributional data from herbarium specimens and specialized literature. Two data matrices were constructed for 60 grid-cells of 2° and 14 biogeographical provinces. The analysis of the 2° grid-cell matrix led to 7084 cladograms. The strict consensus cladogram showed several clades equivalent to the results obtained with the biogeographical provinces. Three clades agree with some principal regions of distribution of Mexican pines, previously identified by several authors, located at the northern portion of the Baja California peninsula, the Sierra Madre Occidental, and the Sierra Madre Oriental. These areas represent important centres of species diversity and endemism for Mexican gymnosperms. The analysis of the province matrix led to two most parsimonious cladograms, which only differed in the position of the Sierra Madre Occidental province. The iterative procedure PAE with progressive character elimination was applied to identify generalized tracks, where clades of provinces were considered equivalent to generalized tracks, and each time a cladogram was obtained, species defining its clades were deleted and a new run was undertaken. We found five generalized tracks, mainly located in montane provinces. The distribution patterns of gymnosperms agree with the existence of several Mexican biogeographical provinces, and a different historical biogeography of the Mexican peninsulas from the rest of the country is evident.  © 2007 The Linnean Society of London, Biological Journal of the Linnean Society , 2007, 92 , 405–417.     

Distributional patterns of the Neotropical humid montane forest avifaunas

The study of biogeographical patterns of the Neotropical humid montane forest avifauna has been prevented due to the lack of phylogenetic hypotheses for most taxa, and to the paucity of detailed studies about the geographical distribution for most of the species. Distributional patterns of this avifauna were explored by integrating predictive distributional models and Parsimony Analysis of Endemicity (PAE). Distributional maps were generated using the Genetic Algorithms for Rule Set Prediction for 442 species; this information was transformed into a data matrix for analysis with PAE. Hierarchical information corresponding to the genus level was incorporated to help resolve the relationships between areas. A strict consensus cladogram showed a clear separation between the Mesoamerican and South American avifaunas. Within the Mesoamerican clade, three geographically structured groups were obtained, whereas the South American clade showed a polytomy of three groups, with two of them, the South Andean Yungas and the Tepuis, located outside the main clade. The third group is a well resolved clade, including areas from eastern Panama and northern Venezuela to central Bolivia. Area relationships suggest a mixed history of dispersal and vicariant events, with the latter being the most important for explaining the biogeographical patterns found.  © 2008 The Linnean Society of London, Biological Journal of the Linnean Society , 2008, 94 , 175–194.     

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.     

An optimality criterion to determine areas of endemism

A formal method was developed to determine areas of endemism. The study region is divided into cells, and the number of species that can be considered as endemic is counted for a given set of cells (= area). Thus, the areas with the maximum number of species considered endemic are preferred. This is the first method for the identification of areas of endemism that implements an optimality criterion directly based on considering the aspects of species distribution that are relevant to endemism. The method is implemented in two computer programs, NDM and VNDM, available from the authors.     

Biogeographical analysis of rodent endemism and distributional congruence in the southern–central Andes (north‐western Argentina)

The recognition of areas of endemism (AEs) is important for conservation biology and biogeographical regionalization. Our objective was to quantitatively identify AEs and distributional congruence patterns of native rodents at the tropical/temperate transition in the central Andes. We analysed 6200 geo‐referenced distributional records of 80 species in north‐western Argentina using NDM/VNDM software. We found 20 AEs defined by 22 endemic species (27% of the total rodent fauna) and 34 patterns of distributional congruence in non‐endemic rodents. Geographical range congruence follows two main patterns running parallel along the Andes. One is related to the humid eastern slopes of the Andes (Argentinean Yungas forest) and the other to the high Andes (Argentinean Puna plateau). Endemism was mainly restricted to the southernmost part of the Yungas forest and adjacent dryer valleys (Monte desert). Species diversity was highest in the northern sector of the Argentinean Yungas forest, where several species reach their southern distributional range. This incongruence among hotspots of diversity and endemism has also been also noted in diversity studies at continental and global scales. Our results provide a starting point for conservation planning in the southernmost Central Andes, which combines the taper of tropical diversity and range‐restricted species endemic to the tropical–temperate transition. © 2014 The Linnean Society of London, Biological Journal of the Linnean Society, 2014, 112 , 163–179.     

Parsimony analysis of endemicity as a panbiogeographical tool: an analysis of Caribbean plant taxa

To demonstrate that parsimony analysis of endemicity (PAE) can be a method implementing the panbiogeographic approach, we analyzed two data matrices of 40/38 biogeographic provinces × 148 plant species from the Caribbean subregion of the Neotropical region, one where taxa are represented by individual tracks and the other where taxa are represented by single sample localities. We obtained six generalized tracks resulted from the PAE of the areas × individual tracks matrix, and one generalized track from the PAE of the areas × single sample localities matrix, with the latter nested within the former tracks. The results obtained show that PAE works as a panbiogeographical tool if it is based on an areas × individual tracks matrix. When performed in this way, PAE retrieves spatial information that is lost when it is based on an areas × single sample localities matrix, raising doubts regarding the conclusions derived from this latter type of analysis. © 2010 The Linnean Society of London, Biological Journal of the Linnean Society, 2010, 101 , 961–976.     

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.     

Phytogeographic analysis of taxa endemic to the Yucatán Peninsula using geographic information systems, the domain heuristic method and parsimony analysis of endemicity

Abstract. The distribution of plant taxa endemic to the Yucatán Peninsula was studied using Parsimony Analysis of Endemicity (PAE). The known distribution of 162 endemic plant taxa was plotted and the DOMAIN method together with environmental data were used to model the potential distribution for each taxon. The Peninsula was divided into a grid of quarter‐degree cells for the purpose of identifying distribution patterns. A total of 294 cells were analysed using known collection records and potential distribution of endemic taxa data. Two data matrices were constructed, a matrix of known distribution and a matrix of both the known and potential distribution. The two matrices were included in the PAE to identify areas of endemism. The areas determined with the known distribution were restricted and almost half of them remained unresolved, whereas with the potential distribution, approximately 90% of the cells were assigned to any one of the endemicity areas. Four endemism areas were identified: the Yucatán dry zone, Yucatán, El Petén and Belize. The areas of Yucatán and El Petén could be explained by current and Pleistocene climatic conditions and their congruence with other biological groups. Analysis of the potential distribution identified areas with patterns that share current environmental characteristics and a palaeoclimate history. Potential distribution modelling can eliminate uncertainties in biogeographical analysis caused by lack of data distribution and sample variation and produce information about the relationships between areas and taxa as well as the environmental affinities of taxa.     

Detecting areas of endemism with a taxonomically diverse data set: plants,mammals, reptiles,amphibians, birds,and insects from Argentina

The idea of an area of endemism implies that different groups of plants and animals should have largely coincident distributions. This paper analyses an area of 1152 000 km², between parallels 21 and 32°S and meridians 70 and 53°W to examine whether a large and taxonomically diverse data set actually displays areas supported by different groups. The data set includes the distribution of 805 species of plants (45 families), mammals (25 families), reptiles (six families), amphibians (five families), birds (18 families), and insects (30 families), and is analysed with the optimality criterion (based on the notion of endemism) implemented in the program NDM/VNDM. Almost 50% of the areas obtained are supported by three or more major groups; areas supported by fewer major groups generally contain species from different genera, families, or orders. © The Willi Hennig Society 2011.     

Endemicity analysis,parsimony and biotic elements: a formal comparison using hypothetical distributions

There is as yet no general agreement regarding the most appropriate solution to the problem of identifying areas of endemism, not even in particular cases. In this study, we compared Endemicity Analysis (EA), Parsimony Analysis of Endemicity (PAE), and Biotic Elements Analysis (BE) based on their ability to identify hypothetical predefined patterns that represent nested, overlapping, and disjoint areas of endemism supported by species with different degrees of sympatry. We found that PAE performs poorly when applied to patterns that either overlap with each other or are supported by species with imperfect sympatry. BE exhibits a counterintuitive sensitivity to the degree of congruence among the distributions of endemic species, being unable to recognize areas of endemism supported by perfectly sympatric species. In contrast, in all cases examined we found that EA results in a high proportion of correctly identified distributional patterns. In addition to highlighting the strengths and limitations of these approaches, our results show how different methods can lead to seemingly conflicting conclusions and caution about the possibility of identifying distributional patterns that are merely methodological artefacts. © The Willi Hennig Society 2012.     

Richness and endemism of helminth parasites of freshwater fishes in Mexico

Distribution records of 152 adult helminth taxa parasites of freshwater fishes in Mexico were analysed to determine areas of high richness and endemism. Distribution maps were prepared for each taxon and overlaid onto a map of Mexico divided into 1 × 1 degree grid-cells. Richness was determined by counting recorded helminth species in each grid-cell. A corrected weighted endemism index was calculated for each grid-cell, and the relationship between richness and endemicity was analysed with an Olmstead–Tukey corner test of association. Five areas of high richness and endemism were identified: (1) Los Tuxtlas and the Papaloapan river basin, on the Gulf of Mexico; (2) the Grijalva-Usumacinta basin near the Gulf of Mexico coastal plain; (3) the Yucatan Peninsula; (4) the Sierra de Manantlán Biosphere Reserve in western Mexico; and (5) the Pátzcuaro lake, in central Mexico. The distribution of richness and endemism of helminth parasites of freshwater fishes in Mexico is congruent with distributional patterns described for other freshwater taxa in Mexico. Patterns of richness and/or endemism in the studied areas can be explained by the ichthyological composition of their bodies of water. The present study establishes an objective way of analysing the relationship between richness and endemicity, and suggests that helminths can make valuable contributions to regionalization of geographical areas and for identification of rich and biologically complex areas with potential for conservation of aquatic systems.  © 2008 The Linnean Society of London, Biological Journal of the Linnean Society , 2008, 94 , 435–444.     

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.     

Parsimony analysis of endemicity and analysis of endemicity: A fair comparison

Parsimony Analysis of Endemicity (PAE) has been compared with other methods regarding its performance to identify areas of endemism. It is frequently compared with the Analysis of Endemicity (AE), which seems to perform better than PAE to identify these areas. Here I compare PAE and AE considering the sympatric taxa diagnosed as endemic, being as strictly close as possible to sympatry, and using previously published data of Sciobius (Coleoptera: Curculionidae). AE identified more candidate areas of endemism than PAE, but the number of highly restricted endemic taxa to these areas was insufficient to support them as areas of endemism. Considering strictly sympatry (homopatry), PAE performed better than AE; however, both methods may identify areas with some grade of sympatry, but the recognition of which areas constitute real areas of endemism in the strict sense depends on the interpretation of the researcher.     

Identification of priority areas for conservation in an arid zone: application of parsimony analysis of endemicity in the vascular flora of the Antofagasta region, northern Chile

Endemic taxa are those restricted to a specific area, and could bedefined as the exclusive biodiversity of a region. An area of endemismcontains taxa found nowhere else and could be catalogued as irreplaceable and of highpriority for conservation. proposed the parsimony analysis of endemicity (PAE) as a tool to detect areas ofendemism. PAE, a method of historical biogeography, is analogous to cladisticmethods used in phylogenetics analysis, and unites areas (taxa in cladistics)based on their shared species (characters in cladistics) according to the mostparsimonious solution. In this paper we determined with PAE, prioritary areasfor conservation on the basis of concentrations of endemic species in the aridregion of Antofagasta, northern Chile, and compared the results with theirrepresentation in the current Chilean National Parks and Reserves System. Wefound two areas suggested as priorities, one located in the north Andean zone ofthe region, and another at the coast. The area with the higher biodiversity andconcentration of endemics was that located at the coast. However, coastalecosystems are currently under-represented in the Chilean National Parks andReserves System. The establishment of a new protected area in the coastal zoneof the region of Antofagasta is currently under consideration, coinciding withthe area suggested with PAE as priority. This new area would not only allowconserving species with evident problems of conservation, but also preserving anarea where higher levels of endemism exist.     

Patterns of richness and endemism of the Mexican herpetofauna,a matter of spatial scale?

The goal of this study was to compare the richness and endemism patterns of Mexican species of amphibians and reptiles at different spatial scales. We used the best available dataset of distributional ranges generated from ecological niche models and employed geographically weighted regressions (GWRs) to test whether richness and endemism were related. Patterns were found to vary with the scale used for richness and endemism, and these patterns were not coincident. The results showed that: (1) only relatively coarse spatial scales can address latitudinal patterns in amphibians and reptiles, and, in fine scales, they are related to topographic formations; (2) areas of greatest endemism for amphibians and reptiles are located in the highlands of the central or southern part of the country, although not necessarily in the same specific highlands for both groups; (3) there is a strong average correlation between richness and endemism for both groups, indicating that the same factors contribute to both patterns, but these factors act differentially in terms of regions among amphibians and reptiles; and (4) the scale at which the analysis is conducted is important, and we believe that careful consideration of spatial scale must be undertaken to avoid false conclusions. © 2013 The Linnean Society of London, Biological Journal of the Linnean Society, 2014, 111 , 305–316.     

Patterns of endemism in south-eastern Pacific benthic polychaetes of the Chilean coast

Aim In this study we evaluate patterns of endemism for benthic polychaete species along the southeastern Pacific coast of Chile. Our goals were (1) to describe latitudinal gradients of endemism and identify areas of high endemism, (2) to evaluate the effect of biogeographical limits on endemism patterns, and (3) to evaluate indirectly the role played by evolutionary dynamics on patterns of endemism. Location South‐eastern Pacific coast of Chile, ranging from Arica (18° S) to Cape Horn (56° S). Methods We used a list of 178 species of endemic, shallow benthic polychaetes to evaluate patterns of endemism. Parsimony analysis of endemicity (PAE) and the endemism index (EI) were used to evaluate hierarchical relationships of endemism between different latitudinal bands, and to identify areas with high degrees of endemism and differences in endemism. We evaluated the effect of biogeographical limits on endemic polychaete fauna by testing for the existence of geometric constraints (mid‐domain effect). The role of evolutionary dynamics on latitudinal patterns of endemism was evaluated with nestedness analysis (NA) using the temperature index. Results The PAE analysis indicated two large, separate areas of endemism: (1) the northern area between 18° S and 38° S, and (2) the southern area between 39° S and 56° S. The endemism index showed a maximum value (32 species) around 39°–41° S. Species‐richness curves of each 3° band of latitude showed a clear mid‐domain effect (69%), but the two maximum points of species richness at mid‐latitudes (36° S to 38° S and 39° S to 41° S) did not correspond to the mid‐domain peak in species richness, presenting a greater number of species than expected by the mid‐domain effect. The nestedness analysis showed that the number of genera reaches a maximum of 70 at mid‐latitudes (36°–41° S), decreasing towards both the northern and southern areas. The spatial distribution of the entire data set of endemic species showed a nested pattern (T° = 24.5°, P < 0.0001). Main conclusions Our results strongly support the existence of a latitudinal gradient of endemism for benthic polychaete species along the Chilean coast. The shape of this gradient is clearly non‐linear, with a marked peak of endemism occurring at mid‐latitudes (36°–41° S, endemism hotspot), which also corresponds to a peak in species richness. Furthermore, this hotspot is the midpoint separating two distinct areas of endemism to the north and south. We suggest that the observed pattern of endemism for benthic polychaete taxa of the Chilean coast can be explained by a combination of geometric constraints and historical mechanisms, such as the processes that affected the Chilean coast during the Neogene (e.g. ENSO, oxygen minimum zone, glaciations).     

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.