Misconceptions about parsimony analysis of endemicity

Nihei, Silvio Shigueo

doi:10.1111/j.1365-2699.2006.01619.x

Cited by 80 publications

(85 citation statements)

References 60 publications

(102 reference statements)

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“…Finally, requirement 3 assured that the distribution of the taxa considered was entirely within the region studied. This avoided the use of partial distributions and wrong interpretations of biogeographic homologies (Nihei 2006).…”

Section: Distributional Datamentioning

confidence: 99%

Detection of areas of endemism on two spatial scales using Parsimony Analysis of Endemicity (PAE): the Neotropical region and the Atlantic Forest

Sigrist

Carvalho

Camargo³

2008

Biota Neotrop.

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An important biological challenge today is the conservation of biodiversity. Biogeography, the study of the distribution patterns of organisms, is an important tool for this challenge. Endemism, the co-occurrence of several species unique to the same area, has important implications for the preservation of biodiversity, since many areas of endemism are also areas with large human impact. More rigorously defined, areas of endemism are historical units of distributional congruence of monophyletic taxa. These areas often assumed to be due to nonrandom historical events that favored conditions associated with high rates of speciation. Thus, understanding endemism and the delimitation of endemic areas has important implications for conservation. Today, most studies delimit areas of endemism by superimposing maps of distribution for various species. This approach suffers from arbitrary delimitations, however, when a great distributional data is used. In this paper we used the method of Parsimony Analysis of Endemicity (PAE) based on georeferenced quadrats in order to delimit areas of endemism. This modality of the method is important due to its testable nature and can also be used to infer area relationships. We applied the method to raw distributional data from 19 unrelated taxa to delimit general patterns of endemism in the Neotropical Region and in the Atlantic forest domain using different grid scales. Neotropical areas found are comprised over the Panama region, northern Andean region and the Atlantic forest. Atlantic forest showed a major division into two distinct components (northern x southern). Endemic areas delimited using smaller scale grids on the Atlantic forest should be considered for conservation priorities once they showed endemism at regional and local scales. The results were also compared to other studies using different taxa and methods. Finally, some considerations on the analysis scale and future perspectives of the method are presented.

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Section: Distributional Datamentioning

confidence: 99%

Detection of areas of endemism on two spatial scales using Parsimony Analysis of Endemicity (PAE): the Neotropical region and the Atlantic Forest

Sigrist

Carvalho

Camargo³

2008

Biota Neotrop.

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“…Humphries, 1989;Humphries, Parenti, 1999;Brooks, Van Veller, 2003;Nihei, 2006). Nonetheless, it has been widely employed in the biogeography of neotropical fishes (cf.…”

Section: Introductionmentioning

confidence: 99%

Biogeography of Amazonian fishes: deconstructing river basins as biogeographic units

2017

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Biogeography of Amazonian fishes (2,500 species in vastly disjunct lineages) is complex and has so far been approached only partially. Here, we tackle the problem on the basis of the largest database yet on geographical distribution and phylogenetic relationships of Amazonian fishes, including all information available. Distributions of 4,095 species (both Amazonian and outgroups) and 84 phylogenetic hypotheses (comprising 549 phylogenetically-informative nodes) were compiled, qualified and plotted onto 46 areas (29 Amazonian and 17 non-Amazonian). The database was analyzed with PAE, CADE, BPA and BPA 0 , yielding largely congruent results and indicating that biogeographic signal is detectable on multiple dimensions of fish distribution, from single species ranges to cladistic congruence. Agreement is especially pronounced in deeper components, such as Trans-Andean, Cis-Andean, Western Amazon and Orinoco basins. Results show that all major Amazonian tributaries, as well as the Amazon basin itself, are non-monophyletic and constitute hybrid sets of heterogeneous biotic partitions. Amazonian drainages should not be assumed a priori as historically cohesive areas, contrary to widespread practice. Our hypothesis allows reevaluation of broader issues in historical biogeography, such as the predictive power of biogeographic hypotheses, the vicariant/ dispersal duality, the significance of widely distributed taxa, and the need for temporal dimension in biogeographic patterns. A biogeografia dos peixes amazônicos (2.500 espécies de diferentes linhagens) é complexa e até agora foi abordada apenas parcialmente. Aqui abordamos o problema com base no maior banco de dados já feito sobre a distribuição geográfica e as relações filogenéticas dos peixes amazônicos, incluindo todas as informações disponíveis. A distribuição de 4.095 espécies (tanto amazônicas como de grupos-externos) e 84 hipóteses filogenéticas (que incluíam 549 nós filogeneticamente informativos) foram compiladas e qualificadas em 46 áreas (29 amazônicas e 17 não-amazônicas). O banco de dados foi analisado a partir das metodologias PAE, CADE, BPA e BPA0, resultando em topologias amplamente congruentes e indicando que o sinal biogeográfico é detectável em múltiplas dimensões, desde a simples distribuição de peixes até em congruência cladística. A concordância topológica é especialmente pronunciada em componentes mais profundos, como as bacias Trans-Andina, Cis-Andina, Amazonas Ocidental e Orinoco. Os resultados demonstram que todos os principais afluentes amazônicos, bem como a própria bacia amazônica, não são monofiléticos e constituem conjuntos híbridos formados a partir de parcelas bióticas heterogêneas. As drenagens amazônicas não devem ser consideradas a priori como áreas historicamente coesas, contrariamente à prática generalizada. Nossa hipótese permite a reavaliação de questões mais amplas na biogeografia histórica, como o poder preditivo de hipóteses biogeográficas, a dualidade vicariante/dispersão, significância de táxons amplamente distribuídos e a n...

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“…Otros autores (Escalante & Morrone, 2003;Nihei, 2006;Morrone, 2009;Echeverry & Morrone, 2010;Escalante, 2011;Crother & Murray, 2013) por su parte lo han defendido en el sentido de que lo consideran un método eficaz para encontrar patrones y, de acuerdo con Ferrari, Barão y Simões (2013) y Morrone (2015), se considera el mejor método para identificar trazos generalizados. Morrone (2014) menciona que muchas de las críticas al PAE se deben a un mal entendimiento de sus bases metodológicas, aunque reconoce que el AE resulta ser más eficiente que el PAE en la identificación de las áreas de endemismo.…”

Section: Discussionunclassified

Evaluación de AE y PAE para identificar trazos generalizados, a partir de las serpientes del estado de Hidalgo, México

Montiel-Canales

Mayer-Goyenechea

Badillo

et al. 2016

RBT

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One of the most important concepts in Panbiogeography is the generalized track, which represents an ancestral biota fragmented by geological events that can be recovered through several methods, including Parsimony analysis of endemicity (PAE) and endemicity analysis (EA). PAE has been frequently used to identify generalized tracks, while EA is primarily designed to find areas of endemicity, but has been recently proposed for identifying generalized tracks as well. In this study we evaluated these methods to find generalized tracks using the distribution of the 84 snake species of Hidalgo. PAE found one generalized track from three individual tracks (Agkistrodon taylori, Crotalus totonacus and Pliocercus elapoides), supported by 89 % of Bootstrap, and EA identified two generalized tracks, with endemicity index values of 2.71-2.96 and 2.84-3.09, respectively. Those areas were transformed to generalized tracks. The first generalized track was retrieved from three individual tracks (Micrurus bernadi, Rhadinaea marcellae and R. quinquelineata), and the second was recovered from two individual tracks (Geophis mutitorques and Thamnophis sumichrasti). These generalized tracks can be considered a unique distribution pattern, because they resembled each other and agreed in shape. When comparing both methods, we noted that both are useful for identifying generalized tracks, and although they can be used independently, we suggest their complementary use. Nevertheless, to obtain accurate results, it is useful to consider theoretical bases of both methods, along with an appropriate choice of the size of the area. Results using small-grid size in EA are ideal for searching biogeographical patterns within geopolitical limits. Furthermore, they can be used for conservation proposals at state level where endemic species become irreplaceable, and where losing them would imply the extinction of unique lineages.

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Misconceptions about parsimony analysis of endemicity

Cited by 80 publications

References 60 publications

Detection of areas of endemism on two spatial scales using Parsimony Analysis of Endemicity (PAE): the Neotropical region and the Atlantic Forest

Detection of areas of endemism on two spatial scales using Parsimony Analysis of Endemicity (PAE): the Neotropical region and the Atlantic Forest

Biogeography of Amazonian fishes: deconstructing river basins as biogeographic units

Evaluación de AE y PAE para identificar trazos generalizados, a partir de las serpientes del estado de Hidalgo, México

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