Out of sight, out of mind: Phylogenetic and taxonomic gaps imply great underestimations of the species’ vulnerability to global climate change

Cordier, Javier Maximiliano; Rojas-Soto, Octavio R.; Semhan, Romina Valeria; Abdala, Cristian Simón; Nori, Javier

doi:10.1016/j.pecon.2021.02.002

Cited by 3 publications

(6 citation statements)

References 32 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Although more sophisticated algorithms progressively replaced ENFA in the mainstream of modelling studies (but see e.g. Andersen et al, 2021; Cartledge et al, 2021; Mugo et al, 2020; Sutton et al, 2021), this method has been used in >200 papers since its publication in 2002 (according to Scopus database in January 2022), and is still widely adopted to describe species habitat preferences, niche characteristics and vulnerability to global change (Cordier et al, 2021; Melchionna et al, 2018; Raia et al, 2020; Rinnan & Lawler, 2019). ENFA marginality and specialization can intuitively be translated into biologically meaningful concepts, as they represent the position and width of a species niche in the environmental space relative to the habitat conditions available to the species (Hirzel et al, 2002).…”

Section: Discussionmentioning

confidence: 99%

ENphylo: A new method to model the distribution of extremely rare species

et al. 2023

View full text Add to dashboard Cite

Species distribution models (SDMs) are a useful mean to understand how environmental variation influences species geographical distribution. SDMs are implemented by several different algorithms. Unfortunately, these algorithms consistently lose accuracy exactly when they are needed the most, that is with rare species, originating the so‐called rare‐species modelling paradox. Although approaches exist to tackle this problem, most notably by performing and then averaging a number of bivariate models, they are usually computationally intensive and were never shown to apply successfully to the rarest species (i.e. with less than 20 geographical occurrences). Here, we present a new algorithm, ENphylo, embedded in the readily‐available R package RRdtn, which couples Environmental Niche Factor Analysis (ENFA) and phylogenetic imputation to model the distribution of rare species. Using the fossil record of 31 species of large mammals that lived during the late Pleistocene as the source data to sample from, we demonstrate ENphylo provides good SDM evaluation scores, with area under the curve and Sørensen Index both consistently above 0.75, True Skills Statistics above 0.4 and Boyce Index above 0.5 in most cases, when just 10 fossil occurrences are randomly drawn from their respective fossil records. ENphylo proved significantly more accurate than ENFA and the ensemble of bivariate models using Maxent, Generalized Linear Model and Random Forest algorithms. Intriguingly, we found that randomly drawing as little as 10 occurrence data points per species allows ENphylo to perform equally well as Maxent run using the entire fossil record of these same species and data. ENphylo provides a fast and accurate solution to perform species distribution modelling with rare species, which will help predicting their distribution in the light of climate change, and to delineate how rare extinct species reacted to past climatic variation.

show abstract

Section: Discussionmentioning

confidence: 99%

ENphylo: A new method to model the distribution of extremely rare species

et al. 2023

View full text Add to dashboard Cite

show abstract

“…This issue is particularly exacerbated in Latin America because there is a lack of enough specialists, which generates geographically unbalanced biodiversity inventories (Hughes et al, 2021; Mora et al, 2011), and a shortage of understanding of population distribution and variation within species (Peterson & Navarro-Sigüenza, 1999), increasing the Linnean, Darwinian, and Wallacean shortfalls (Hortal et al, 2015). However, recently re-analyzed groups based on formal phylogenetic methods reveal that the actual diversity patterns are usually underestimated (Cordier et al, 2021). Therefore, splitting/synonymizing the species groups (filling Linnean and Darwinian shortfalls), generates immediate changes in species distributions (filling Wallacean shortfalls; Diniz-Filho et al, 2013; Hortal et al, 2015).…”

Section: Introductionmentioning

confidence: 99%

“…By applying the PSC delimitation criteria instead of the BSC in the risk lists, different allopatric and diagnosable populations within some of the current biological species would be recognized as independent evolutionary units (Rojas-Soto et al, 2010). Consequently, several taxa considered as subspecies under the BSC would be considered as species under the PSC since biological species could be divided into two or more phylogenetic species (Figure 1a), which means recognizing independent distribution areas (i.e., allopatric populations recognized as separate species; Cordier et al, 2021; Zink, 2014). This division implies that, when applying the PSC, a reevaluation for the assignment of the risk categories is needed in some cases, given the presumption that they could be at greater risk due to the intrinsic reduction of the distribution areas and their population sizes (Cordier et al, 2021; Rojas-Soto et al, 2010; Williams et al, 2009).…”

Section: Introductionmentioning

confidence: 99%

“…Consequently, several taxa considered as subspecies under the BSC would be considered as species under the PSC since biological species could be divided into two or more phylogenetic species (Figure 1a), which means recognizing independent distribution areas (i.e., allopatric populations recognized as separate species; Cordier et al, 2021; Zink, 2014). This division implies that, when applying the PSC, a reevaluation for the assignment of the risk categories is needed in some cases, given the presumption that they could be at greater risk due to the intrinsic reduction of the distribution areas and their population sizes (Cordier et al, 2021; Rojas-Soto et al, 2010; Williams et al, 2009). In this sense, one might expect that the consideration of subspecies for protection would not represent a conservation problem if subspecies always agreed with phylogenetic species or evolutionary units (e.g., Glaucidium griscomi corresponds with Glaucidium palmarum griscomi ) but this becomes problematic when subspecies do not correspond with phylogenetic species (e.g., the phylogenetic species Glaucidium palmarum include two subspecies: G. palmarum palmarum , and G. p. oberholseri ), which masks the actual conservation target (Figure 1a).…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Implications on the Use of the Phylogenetic Species Concept in the Risk Categories Assignment: The Case of the Birds of Mexico

Galindo-Cruz

Sahagún-Sánchez

Rojas‐Soto

2022

Tropical Conservation Science

Self Cite

View full text Add to dashboard Cite

Background and Aims Conservation efforts require a rational basis for taxa prioritization; it is essential to recognize the evolutionary independence of units, typically recognized as species. Because different criteria on species limits lead to different conservation assessment priorities, conceptual problems limit the possibility to accurately assess the conservation status that species are undergoing to protect them effectively. Methods We analyze the implications of using the phylogenetic species concept (PSC) in the risk categories determination, based on the analysis of the Mexican endemic avifauna. We modeled the potential distribution areas with the MaxEnt algorithm for those species that have had or could be susceptible to taxonomic updates based on the PSC. Results Of the 93 studied species, 68 were highly restricted, and 23 have high scores according to the evaluation of the Partners In Flight conservation status, so they can be considered species with high vulnerability or risk of extinction. Additionally, based on the recognition of several allopatric populations as independent phylogenetic species, 45% are susceptible to reconsideration of their risk categories due to a decrease in the extent of areas where they are potentially distributed. Implications for Conservation The use of a taxonomic perspective focused on the phylogenetic relationship of the different populations would directly impact the definition of risk categories, particularly for those endemic or restricted distribution evolutionary units for which there is usually very little information available and which, undoubtedly, are the ones that most need to be studied and, particularly, protected.

show abstract

“…In these historical processes, the area where Colombia is currently located has played a significant role as a mid-point between Central and South America (Samper, 1998;Jaramillo & Oviedo, 2017). For this reason, studies with considerable sampling gaps address the evolutionary history of lineages partially only, and may be masking genetic structure or species threats (Hillis, 2019;Chambers & Hillis 2020, Cordier et al 2021. Additionally, these sampling gaps may cause taxonomic instability, since the identity of the unsampled taxa or of taxa in unsampled regions are normally ignored or questioned but not resolved, therefore increasing the number of paraphyletic groups or species complexes.…”

mentioning

confidence: 99%

Inclusion Is Not Representativeness: The Context of Colombian Samples in the Taxonomic and Systematic Mid-Large Herpetological Literature

Vásquez‐Restrepo¹

2021

Rev Latin Herp

View full text Add to dashboard Cite

Despite being one of the most biodiverse countries in the world, the inclusion and representativeness of samples from Colombia in taxonomic and systematic studies are still low in the herpetological literature. Currently, there are 80 herpetological collections in Colombia, which house more than 214 000 specimens with wide geographic coverage and extensive metadata. Here, I review the main herpetological literature in the Neotropics for the last 20 years, to explore the inclusion and representativeness of Colombian samples in taxonomic and systematic studies. I also compile the data available in Colombian herpetological collections, to provide a picture of its current status. I found that quantifying the inclusion and representativeness requires an indirect approach, since their dependence on the taxa distribution and sample availability mask the true extent of the gaps. Then, I discuss five possible reasons that may explain this phenomenon, including the absence of data, how bureaucracy may constrain researchers, the visibility of the data through online platforms, the participation of local taxonomists in publications, and difficulties accessing the existing material. I close with a discussion of the consequences and possible solutions.

show abstract

Out of sight, out of mind: Phylogenetic and taxonomic gaps imply great underestimations of the species’ vulnerability to global climate change

Cited by 3 publications

References 32 publications

ENphylo: A new method to model the distribution of extremely rare species

ENphylo: A new method to model the distribution of extremely rare species

Implications on the Use of the Phylogenetic Species Concept in the Risk Categories Assignment: The Case of the Birds of Mexico

Inclusion Is Not Representativeness: The Context of Colombian Samples in the Taxonomic and Systematic Mid-Large Herpetological Literature

Contact Info

Product

Resources

About