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.     

Do Rapoport's rule,the mid‐domain effect or the source–sink hypotheses predict bathymetric patterns of polychaete richness on the Pacific coast of South America?

Aim We evaluated the bathymetric gradient of benthic polychaete species richness from the Chilean coast, as well as its possible underlying causes. We tested three possible hypotheses to explain the richness gradient: (1) Rapoport's effect; (2) the mid‐domain effect (MDE); and (c) the source–sink hypothesis. Location South‐eastern Pacific coast of Chile. Methods The bathymetric gradient in richness was evaluated using the reported ranges of bathymetric distribution of 498 polychaete species, from the intertidal to abyssal zone (c. 4700 m). Rapoport's effect was evaluated by examining the relationship between bathymetric mid‐point and bathymetric range extent, and species richness and depth. The MDE was tested using the Monte Carlo simulation program. The source–sink hypothesis was tested through nestedness analysis. Results Species richness shows significant exponential decay across the bathymetric gradient. The pattern is characterized by a high presence of short‐ranged species on the continental shelf area; while only a few species reach abyssal depths, and they tend to show extremely wide bathymetric ranges. Our simulation analyses showed that, in general, the pattern is robust to sampling artefacts. This pattern cannot be reproduced by the MDE, which predicts a parabolic richness gradient. Rather, results agree with the predictions of Rapoport's effect. Additionally, the data set is significantly nested at species, genus and family levels, supporting the source–sink hypothesis. Main conclusions The sharp exponential decay in benthic polychaete richness across the bathymetric gradient supports the general idea that abyssal environments should harbour fewer species than shallower zones. This pattern may be the result of colonization–extinction dynamics, characterized by abyssal assemblages acting as ‘sinks’ maintained mainly by shallower ‘sources’. The source–sink hypothesis provides a conceptual and methodological framework that may shed light on the search for general patterns of diversity across large spatial scales.     

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.     

Biogeographical patterns and Rapoport's rule in southeastern Pacific benthic polychaetes of the Chilean coast

Recently three biogeographical units were identified along the Chilean coast (the Magellanic Province, an Intermediate Area, and the Peruvian Province), however few studies have focused on the factors and dynamic processes that formed these spatial units (e.g. Rapoport's rule and its causal mechanisms). In this study we used benthic polychaetes of the Chilean coast to evaluate patterns of latitudinal distribution and species richness, and the existence of the three main biogeographical provinces described for the Chilean coast. Additionally, we evaluated the latitudinal Rapoport effects and geometric constraint as a null hypothesis explaining the species richness distribution.
We found that benthic polychaete diversity increased towards southern latitudes. The cluster and ordination (non-metric MultiDimensional Scaling, nMDS) analyses of the distribution data, presented only two statistically significant (bootstrapping techniques) biogeographic provinces along the Chilean coast, with a break occurring between 41° and 42°S. While, our results did not support a latitudinal Rapoport effect, they did support the view that latitudinal Rapoport effects are a local phenomenon, occurring only for the Northeastern Pacific marine taxa. The relationship between latitudinal range extent and mean latitude indicated the existence of two hard boundaries at either extreme of the Chilean coast, limiting the geographical ranges of the species. However, geometric constraints tested using a Monte Carlo simulation approach showed a weak level of mid-domain effect on species richness. Finally, we propose that geometric constraint together with the geomorphology and historical characteristics of the Chilean coast explain the biogeographical patterns of benthic polychaete taxa in Chile.     

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.     

Areas of endemism of Mexican mammals: reanalysis applying the optimality criterion

In order to test Mexican areas of endemism of mammals identified by previous parsimony analyses of endemicity (PAEs), we applied the optimality criterion to three data matrices (based on point records, potential distributional models and the fill option in software NDM). We modelled the ecological niches of 429 terrestrial mammal species using the genetic algorithm for rule-set prediction (GARP) and models were projected as potential distributional areas. We overlapped the point occurrence data and the individual maps of potential distributions to a grid of 1° latitude–longitude. Three matrices of 247 grid cells (areas) and 429 species were built: (1) a binary matrix with '0' for absence and '1' for presence of at least one record of the species inside the grid-cell; (2) a three-state matrix similar to (1) but assigning the state '2' to the assumed presence in the model of potential distribution; and (3) a three-state matrix similar to (2), but applying the fill option of software NDM instead of using a model. The optimality criterion was performed in NDM version 2.7 and results were examined with VNDM version 2.7. The first and second matrices showed 13 areas of endemism and the third identified 16 areas of endemism. NDM provided a better resolution than PAE, allowing us to identify several new areas of endemism, previously undetected. Ecological niche models, projected as potential distributional areas, and the optimality criterion are very useful to identify areas of endemism, although they should be used with caution because they may overpredict potential distributional areas. PAE seems to underestimate the areas of endemism identified.  © 2009 The Linnean Society of London, Biological Journal of the Linnean Society , 2009, 98 , 468–478.     

Patterns and causes of species richness: a general simulation model for macroecology

Understanding the causes of spatial variation in species richness is a major research focus of biogeography and macroecology. Gridded environmental data and species richness maps have been used in increasingly sophisticated curve‐fitting analyses, but these methods have not brought us much closer to a mechanistic understanding of the patterns. During the past two decades, macroecologists have successfully addressed technical problems posed by spatial autocorrelation, intercorrelation of predictor variables and non‐linearity. However, curve‐fitting approaches are problematic because most theoretical models in macroecology do not make quantitative predictions, and they do not incorporate interactions among multiple forces. As an alternative, we propose a mechanistic modelling approach. We describe computer simulation models of the stochastic origin, spread, and extinction of species’ geographical ranges in an environmentally heterogeneous, gridded domain and describe progress to date regarding their implementation. The output from such a general simulation model (GSM) would, at a minimum, consist of the simulated distribution of species ranges on a map, yielding the predicted number of species in each grid cell of the domain. In contrast to curve‐fitting analysis, simulation modelling explicitly incorporates the processes believed to be affecting the geographical ranges of species and generates a number of quantitative predictions that can be compared to empirical patterns. We describe three of the ‘control knobs’ for a GSM that specify simple rules for dispersal, evolutionary origins and environmental gradients. Binary combinations of different knob settings correspond to eight distinct simulation models, five of which are already represented in the literature of macroecology. The output from such a GSM will include the predicted species richness per grid cell, the range size frequency distribution, the simulated phylogeny and simulated geographical ranges of the component species, all of which can be compared to empirical patterns. Challenges to the development of the GSM include the measurement of goodness of fit (GOF) between observed data and model predictions, as well as the estimation, optimization and interpretation of the model parameters. The simulation approach offers new insights into the origin and maintenance of species richness patterns, and may provide a common framework for investigating the effects of contemporary climate, evolutionary history and geometric constraints on global biodiversity gradients. With further development, the GSM has the potential to provide a conceptual bridge between macroecology and historical biogeography.     

Areas of endemism of the Patagonian steppe: an approach based on insect distributional patterns using endemicity analysis

Aims  To delimit areas of endemism in the Patagonian steppe using endemicity analysis (EA), which evaluates areas of endemism by means of an endemicity index, and to compare the resulting endemic areas with those proposed for the Patagonian steppe by previous authors.
Location  The Patagonian steppe, a region of South America found approximately below parallel 36° S to the east of the Andes Mountains.
Methods  Distributional data for 159 species of insects collected in the Patagonian steppe, and consisting of 1317 georeferenced samples were used to identify areas of endemism. A data grid of presence and absence (with cells of 1° × 1°) was constructed. Initially, two different types of EA were performed, seeking areas defined by 'four or more' species. A first analysis was performed without taking into consideration those quadrats where no species had been recorded (empty quadrats), which in many cases meant a discontinuous distribution. The second analysis was performed assuming a continuous distribution for each species. A third analysis, assuming continuous distributions, was performed using 'three or more' as the number of species necessary for an area to be identified as an endemic area.
Results  In the first two analyses, EA recognized the same five areas of endemism: western Patagonia, south-western Payunia, northern Suabandean, southern Subandean and Austral Patagonia. The results of the third analysis allowed the identification of three more areas of endemism: northern Payunia, Chubutian and Santacrucian.
Main conclusions  We identified five areas of endemism for the Patagonian steppe, some of which have been defined in previous contributions. These areas are: Western Patagonia, Payunia and Subandean Patagonia (which can be divided into septentrional and meridional), Central Patagonia (Chubutence and Santacrucense) and Austral Patagonia.     

中国斑腿蝗科特有种的分布及特有分布区划分

按照150km×150km对中国陆地部分进行栅格划分,收集整理了中国斑腿蝗科237个特有种在各栅格的分布信息,建立了物种(237)×栅格(168)数据矩阵,研究了中国斑腿蝗科特有种的分布规律并用PAE法进行特有分布区划分。结果表明:除天山山地分布的少数几个种外,中国斑腿蝗科特有种基本分布西南-东北走向。在该范围内南多北少。华南和西南是中国斑腿蝗科特有种最丰富的地区,在秦巴山区、藏东南和浙闽丘陵地带各有一个高密度的分布区。11个特有分布区中5个分布在东洋界部分,两个在中国东部古北和东洋界交界区,天山山地有一个分散的特有分布区,东北有2个特有分布区。特有分布区的分布和划分基本和中国动物地理区划及区系相一致,但台湾地区归入华中区;横断山和秦岭山地的栅格在支序图中多形成未决分类单元,特有分布区划分困难;华南和华中地区的特有分布区可以进一步划分成更小范围的特有分布区;从云南西北的腾冲、保山经过贵州南部到广西桂林的一个东西狭长的区域可以作为一个特有分布区     

Biogeography of salt marsh plant zonation on the Pacific coast of South America

Aim

The aim of this study was to investigate the biogeography of plant zonation in salt marshes on the Pacific coast of South America; to examine whether salt marsh plant zonation varies with latitude; and to explore the relative importance of climatic, tidal, edaphic and disturbance factors in explaining large‐scale variation in salt marsh plant community structure.

Location

A 2,000‐km latitudinal gradient on the Pacific coast in Chile, with a climate shift from hyper‐arid at low to hyper‐humid at high latitudes.

Methods

Plant zonation was quantified in field surveys of ten marshes. Climate, tidal regimes, edaphic factors and disturbances (tsunami and rainfall floods) were determined. We used multivariate analyses to explore their relative importance in explaining large‐scale variation in salt marsh plant community structure.

Results

Across latitude, marshes were dominated by distinct plant communities in different climate regions, especially at the extreme dry and wet latitudes. Intertidal plant species zonation was present in hyper‐arid and semi‐arid climates, but not in arid, humid and hyper‐humid climates. Latitudinal variation in low‐marsh plant communities (regularly flooded at high tide) was largely a function of precipitation, while at high marshes (never flooded at high tide) latitudinal variation was explained with precipitation, temperature, tidal cycles, soil salinity and disturbances.

Main conclusions

Salt marshes on the Pacific coast of South America belong to Dry Coast and Temperate biogeographic types. Salt marsh plant zonation varies across latitude, and is explained by climatic, tidal, edaphic and disturbance factors. These patterns appear to be mechanistically explained by extrapolating experimentally generated community assembly models and have implications for predicting responses to climate change.     

The coincidence of rarity and richness and the potential signature of history in centres of endemism

We investigate the relative importance of stochastic and environmental/topographic effects on the occurrence of avian centres of endemism, evaluating their potential historical importance for broad‐scale patterns in species richness across Sub‐Saharan Africa. Because species‐rich areas are more likely to be centres of endemism by chance alone, we test two null models: Model 1 calculates expected patterns of endemism using a random draw from the occurrence records of the continental assemblage, whereas Model 2 additionally implements the potential role of geometric constraints. Since Model 1 yields better quantitative predictions we use it to identify centres of endemism controlled for richness. Altitudinal range and low seasonality emerge as core environmental predictors for these areas, which contain unusually high species richness compared to other parts of sub‐Saharan Africa, even when controlled for environmental differences. This result supports the idea that centres of endemism may represent areas of special evolutionary history, probably as centres of diversification.     

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.     

Identification of the areas of endemism (AOEs) of the genus Acantholimon (Plumbaginaceae) in Iran

Abstract

This study was conducted to identify areas of endemism for Acantholimon species using parsimony analysis of endemicity (PAE) and to detect endemic species richness of the genus in the region. The results obtained from the two methods used in this study were used in determining the priorities for the conservation of Acantholimon species in Iran. The distribution database of 62 endemic species belonging to this genus was formed by 1250 georeferenced observations in Iran. The study area was divided into 1?×1? grids of operative geographical units (OGUs) and the species?×?area matrix including presence/absence data was created. The endemic species richness was calculated using circular neighborhood with a radius of 50?km in 10?×?10?km² raster cells using DIVA-GIS software. The results of PAE analysis have shown four areas of endemism (AOEs) in Iran. AOE1: including Alborz and Zagros mountains, the mountains of central Iran. AOE2 and AOE3 are located in Khorassan subregion and AOE4 contains parts of western Iran. The map of endemic species richness indicated that the highest number of endemic species occurs in central Alborz region as well as Kerman, Chahar-Mahal and Bakhtiari, and Isfahan provinces.     

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.     

Patterns in the diversity and endemism of extant Eocene age lineages across southern Africa

Southern Africa boasts a wealth of endemic fauna and flora, comprising both massive recent radiations such as those characteristic of the Cape flora, and solitary ancient species such as the peculiar desert gymnosperm Welwitschia. This study was undertaken to identify ancient biological lineages (tetrapod and vascular plant lineages of Eocene age or older) endemic to southern Africa, and to map their distribution across the region. Twenty‐seven (17 plant and ten animal) lineages were identified, and distribution maps were generated for each of them across 74 operational geographic units, which were then combined into total endemism and corrected weighted endemism per unit area. Total endemism peaked along South Africa's coast and Great Escarpment, but in the case of weighted endemism high values were also recorded along other portions of the Great Escarpment further north. A review of the lineages sister to southern African ancient endemic lineages showed that these are often globally widespread, and many of them differ substantially from the southern African ancient lineages in terms of morphology and ecology. The mechanisms of ancient lineage survival in the region are discussed, and their importance for conservation in southern Africa is emphasised.     

Patterns of endemism in riverine fish of the Northern Hemisphere

Loss of endemic species represents a symptom of general degrading ecosystem conditions that is the indirect result of biodiversity alteration. Here, we developed a predictive model relating species richness of endemic riverine fishes to measured biological, climatic, and historical variables using data from 118 rivers distributed all over the Northern Hemisphere. In a minimally adequate multiple general least square model, total riverine fish species richness, historical biogeography (Pleistocene glaciations), and comtemporary climate accounted for 63% of the variability in endemic species richness; the strongest correlate being riverine fish species richness. Our findings suggest that (i) endemism and richness patterns are generally similar (fish diversity "hot-spots" areas sustain higher endemic species richness); (ii) glaciation in the Pleistocene have had a significant negative influence on endemic species richness in the more septentrional areas; and (iii) certain basins situated in desertic areas (subtropical dry-zone of deserts) have unusually high numbers of endemics. These last areas should not be overshadowed when setting conservation priorities.     

Endemic tenebrionids (Coleoptera: Tenebrionidae) from the Patagonian steppe: a preliminary identification of areas of micro‐endemism and richness hotspots

Based on data from sixteen museum collections we listed the endemic tenebrionids that inhabit the Patagonian steppe. Then, according to the geographical location of the species, we identified areas of micro‐endemism and hotspots within this biogeographic province. Results showed 115 endemic tenebrionid species from the Patagonian steppe, 25 areas of micro‐endemism and five hotspots. We used these outcomes to identify areas of importance for conservation. Based on the comparison with other biogeographic provinces, we suggest that the Patagonian steppe constitutes a center of high endemism for tenebrionids. We hypothesize that the isolation of the Patagonian steppe from other arid areas would cause the high occurrence of endemism. In addition, we suggest processes that could be responsible for the origin of the areas of micro‐endemism and hotspots identified in this work.     

Transit towards floristic homogenization on oceanic islands in the south-eastern Pacific: comparing pre-European and current floras

Aim  To quantify the occurrence of processes of homogenization or differentiation in the vascular flora of six oceanic islands.
Location  Six islands in the south-eastern Pacific drawn from the Desventuradas Archipelago, Easter Island and the Juan Fernández Archipelago.
Methods  Using published floristic studies, we determined the floristic composition of each island at two different stages: (1) pre-European colonization and (2) current flora. We compared changes in the number of shared plants and the floristic similarity among islands for each stage.
Results  The number of plant species doubled from 263 in pre-European flora to 531 species currently. Only three native species became extinct, four natives were translocated among the islands and 271 plant species were introduced from outside. The frequency of plant species shared by two or more islands is higher in the post-European floras than prior to European contact, and the level of floristic similarity between islands increased slightly.
Main conclusions  Considering the low naturalization rate of alien plants, the small number of extinctions and the meagre increase in floristic similarity, these islands are undergoing a slow process of floristic homogenization.