Integrating phylogeography and ecological niche modelling to test diversification hypotheses using a Neotropical rodent

Machado, Arielli Fabrício; Nunes, Mario da Silva; Silva, Cláudia Regina da; Santos, Marcelo Augusto dos; Farias, Izeni Pires; Silva, Maria Nazareth Ferreira da; Anciães, Marina

doi:10.1007/s10682-019-09968-1

Cited by 22 publications

(15 citation statements)

References 113 publications

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“…Similarly, the diversification of the Amazonian lineages was probably determined primarily by the formation and dynamics of the rivers of the Amazon basin, which form barriers to gene flow between L. coronata populations, as also observed in other groups of organisms, such as birds (Fernandes et al, ; Ribas et al, ), primates (Cortéz‐Ortiz et al, ), rodents (Machado et al, ) and reptiles (Geurgas & Rodrigues, ). The initial diversification of the Amazonian populations of L. coronata occurred at approximately 0.9 mya (species tree) through a second vicariant event, which resulted in the formation of lineage C and the ancestor of the sister lineages, A and B.…”

Section: Discussionmentioning

confidence: 86%

Multilocus data of a manakin species reveal cryptic diversification moulded by vicariance

et al. 2019

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We used molecular tools and a multilocus approach to investigate the phylogeography of Lepidothrix coronata across most of its ample range. We sequenced six DNA fragments to produce phylogenies, molecular dating estimates, analyses of the dynamics of the demographic history of the species and a biogeographic analysis to estimate the events and changes in the ancestral distribution of the species. The results indicated the presence of four well‐established lineages, with high levels of divergence. These lineages are delineated by well‐defined geographic barriers, with one lineage, restricted to the west of the Andes, being the first to diverge from the complex. The other three lineages are exclusive to the Amazonian distribution of the species, with two being found north of the Amazon River, and the third, south of the Amazon. Some of the relationships found between these lineages were distinct from those described in previous studies. Important disagreements were found between the mtDNA phylogeny and that of the multilocus analysis, in relation to the lineages located to the west of the Andes. We propose that past introgression events may have influenced shifts in the relationships between lineages, despite the fact that the groups were well defined in both the phylogenies. The biogeographic analysis indicates that the lineages arose through successive vicariance events, which had a primary role in the diversification of the group. Two or three genetically structured subclades were also found within each Amazonian lineage, although these subclades are not isolated by an obvious geographic barrier.

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Section: Discussionmentioning

confidence: 86%

Multilocus data of a manakin species reveal cryptic diversification moulded by vicariance

et al. 2019

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“…Many literatures have modeled the ecology of prehistoric species using pollen records (Meadows 2007, Qiu et al 2020, climate, and ecological niche modeling (Machado et al 2019). One of successful attempts can be seen from works by Ulker et al (2018) on pedunculate oak (Quercus robur) during…”

Section: Discussionmentioning

confidence: 99%

Suitable Habitat Modeling of Prehistoric Antelope-like Bovid <em>Duboisia Santeng</em> in Java Island in The Early Pleistocene

Wibowo¹

2020

Preprint

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The migration routes have facilitated the distribution of mammals from south east Asian mainland to the Sundaland including Java island in the early Pleistocene. One of species that has migrated through that route is antelope-like bovid Duboisia santeng. In the present study, the potential distribution areas and the suitable habitats of D. santeng have been projected and modeled. The modeled habitat was a forest river basin sizing 302.91 Ha in the central of Java island. The model has classified and reconstructed the habitat suitability ranged from low to high back to Pleistocene. The surrounding areas of forest were mostly classified as medium and low related to the limited tree covers. Most suitable habitats were identified in the middle of forest river basin where the tree covers were presented

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“…On the other hand, occurrence records are commonly grouped in areas with greater sampling effort, which may result in spatial autocorrelation. Numerous studies have used spatial filtering to avoid spatial autocorrelation by excluding records very close to each other (Boria, Olson, Goodman, & Anderson, ; Machado et al, ). Spatial filtering reduces overfitting effects, which occurs when the model is too tightly adjusted to calibration data and cannot predict data accuracy independently (Radosavljevic & Anderson, ).…”

Section: Methodsmentioning

confidence: 99%

Section: Data Treatmentmentioning

confidence: 99%

Improving conservation strategies of raptors through landscape ecology analysis: The case of the endemic Cuban Black Hawk

Ferrer-Sánchez

Rodríguez‐Estrella

Martínez-Morales³

2019

Ecology and Evolution

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Raptor species conservation should consider a landscape perspective in order to include habitat requirements associated to large home ranges around nesting sites. Landscape analysis can help to better understand raptor habitat requirements and the degree of tolerance to habitat changes at different scales. We used a landscape ecology perspective to determine the nesting habitat selection of endemic and endangered Cuban Black Hawk, and using ecological niche modeling, we obtained the potential distribution of nests to evaluate the effectiveness of protected areas (PAs) for raptor conservation. Nesting habitat selection was related to breeding success at a landscape scale using data from 27 different nesting sites during 2012–2013 breeding seasons. The potential nesting areas distribution was compared with current officially PAs design in the central region of Cuba. All nests were located in mangrove swamp. Pairs chose nesting sites with low soil–vegetation moisture and low soil reflectance. At the landscape level, they selected low shape complexity of patches and few patches of coastal vegetation around nesting sites which contained similar mangrove patch size and shape. The potential distribution of nests increased close to the coastline. The model predicted a suitable narrow area of 556 km2, and the most favorable nesting area represented 2% of this total. 33% of nests were located within officially natural protected areas while 27% were close to or inside highly threatened areas. A 16% of high to medium suitable nesting habitat overlaps with urban areas. Currently, PAs contain 23% of the nesting area distribution. Our study shows landscape ecology and nest‐site selection approach is crucial to evaluate the persistence of Cuban Black Hawk, as environmental variables and human activity can be related to its productivity. This approach can be applied in conservation strategies of island raptors.

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Integrating phylogeography and ecological niche modelling to test diversification hypotheses using a Neotropical rodent

Cited by 22 publications

References 113 publications

Multilocus data of a manakin species reveal cryptic diversification moulded by vicariance

Multilocus data of a manakin species reveal cryptic diversification moulded by vicariance

Suitable Habitat Modeling of Prehistoric Antelope-like Bovid <em>Duboisia Santeng</em> in Java Island in The Early Pleistocene

Improving conservation strategies of raptors through landscape ecology analysis: The case of the endemic Cuban Black Hawk

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