Cloudy with a chance of speciation: integrative taxonomy reveals extraordinary divergence within a Mesoamerican cloud forest bird

Venkatraman, Madhvi X.; DeRaad, Devon A.; Tsai, Whitney L. E.; Zarza, Eugenia; Zellmer, Amanda J.; Maley, James M.; McCormack, John E.

doi:10.1093/biolinnean/bly156

Cited by 31 publications

(13 citation statements)

References 67 publications

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“…This species is restricted to Mesoamerican cloud forest patches, and as a consequence has a distribution that is highly fragmented. Our simulations suggest that populations of this species would have been highly connected under Last Glacial Maximum conditions, which contradicts recently published indications that the different geographic isolates of the species are highly differentiated (Venkatraman et al 2019). As such, we suspect that dispersal ability in this species is minimal, perhaps even lower than the lowest dispersal setting that we explored in our simulations.…”

Section: Aphelocoma Jay Biogeographycontrasting

confidence: 94%

A simulation-based method for selecting calibration areas for ecological niche models and species distribution models

Machado‐Stredel¹,

Cobos²,

Peterson³

2021

Frontiers of Biogeography

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Ecological niche models and species distribution models (ENM and SDM, respectively) are tools that have seen massive use and considerable improvement during the last twenty years. The choice of calibration areas for such models has strong effects on model outcomes and model interpretation, as well as on model transfer to distinct environmental settings. However, approaches to selecting these areas remain simple and/or unlinked to biological concepts. Such models should be calibrated within areas that the species of interest has explored throughout its recent history, the accessible area (M). In this paper, we provide a simulation approach for estimating a species' M considering processes of dispersal, colonization, and extinction in constant current climate or glacial-interglacial climate change frameworks, implemented within a new R package we developed called grinnell. Using the avian genus Aphelocoma, we explored different parameterizations of our simulation, and compared them to current approaches for M selection, in terms of model performance and risk of extrapolation using the algorithm Maxent and mobility-oriented parity analyses. Model calibration exercises from all approaches resulted in at least one model meeting optimal performance criteria for each species; however, we noted high variability among taxa and M selection methods. More importantly, M hypotheses derived directly from simulations of key biological processes, rather than being based on simple proxies of those processes, and as such are better suited to erecting biologically appropriate contrasts in model calibration, and to characterizing the potential for model extrapolation more rigorously. Major factors in our simulations were environmental layer resolution, dispersal kernel characteristics, and the inclusion of a changing framework of climatic conditions. This contribution represents the first simulation-based method for selecting calibration areas for ENM and SDM, offering a quantitative approach to estimate the accessible area of a species while considering its dispersal ability, along with patterns of change in environmental suitability across space and time. Highlights! We present a simulation-based method to delimit areas that have been accessible for species during relevant periods of time (M) and that represent appropriate calibration areas in ecological niche modeling and species distribution modeling. ! We explored implications of using calibration areas, created with common methods and simulations, on performance of models and on their predictions. ! Our results show that simulated M areas differ in geographic pattern and extent from those created with other methods. ! Although M areas derived from simulations are still hypotheses, they are closer to the regions that could have been explored by a species; comparisons of model outputs showed that these differences have effects in model prediction and interpretation.

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Section: Aphelocoma Jay Biogeographycontrasting

confidence: 94%

A simulation-based method for selecting calibration areas for ecological niche models and species distribution models

Machado‐Stredel¹,

Cobos²,

Peterson³

2021

Frontiers of Biogeography

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“…However, we acknowledge that the Calandrella larks are poorly differentiated morphometrically (Figure 1), and we stress that other types of data, in combination with dense taxon sampling, are necessary for confident taxonomic revisions. Here, we lack substantive data from nuclear DNA markers, vocalizations, other behaviours, ecology etc., to take the fully integrative taxonomic approach [108][109][110] that is becoming more common, e.g., [111][112][113][114][115][116][117][118][119][120] and which we argue should be the gold standard. Yet, while we emphasize that taxonomic decisions should never rest on mitochondrial trees alone [101,106], we here make use of available morphometric data and evaluate a recent tool for single-locus molecular species delimitation [54], which has been used to propose avian taxonomic revisions based solely on mitochondrial data [121] or in combination with morphometry [65].…”

Section: Reliability Of Molecular Species Delimitationmentioning

confidence: 99%

Molecular Species Delimitation of Larks (Aves: Alaudidae), and Integrative Taxonomy of the Genus Calandrella, with the Description of a Range-Restricted African Relic Taxon

et al. 2020

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Larks constitute an avian family of exceptional cryptic diversity and striking examples of convergent evolution. Therefore, traditional morphology-based taxonomy has recurrently failed to reflect evolutionary relationships. While taxonomy ideally should integrate morphology, vocalizations, behaviour, ecology, and genetics, this can be challenging for groups that span several continents including areas that are difficult to access. Here, we combine morphometrics and mitochondrial DNA to evaluate the taxonomy of Calandrella larks, with particular focus on the African C. cinerea and the Asian C. acutirostris complexes. We describe a new range-restricted West African taxon, Calandrella cinerea rufipecta ssp. nov. (type locality: Jos, Plateau State, Nigeria), with an isolated relic population 3000 km from its closest relative in the Rift Valley. We performed molecular species delimitation, employing coalescence-based multi-rate Poisson Tree Processes (mPTP) on cytochrome b sequences across 52 currently recognized lark species, including multiple taxa currently treated as subspecies. Three species-level splits were inferred within the genus Calandrella and another 13 across other genera, primarily among fragmented sub-Saharan taxa and taxa distributed from Northwest Africa to Arabia or East Africa. Previously unknown divergences date back as far as to the Miocene, indicating the presence of currently unrecognized species. However, we stress that taxonomic decisions should not be based on single datasets, such as mitochondrial DNA, although analyses of mitochondrial DNA can be a good indicator of taxa in need of further integrative taxonomic assessment.

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“…During this period, the climatic variations between cold and warm cycles resulted in expansions and contractions of the TMCF due to the species dependency to the high atmospheric humidity (Ramírez-Barahona & Eguiarte, 2013). These processes led to complex patterns of connectivity and fragmentation on species distributions, evolutionary adaptations to local environmental conditions and lineage divergence in plant and animal populations (Gutiérrez-Rodríguez, Ornelas & Rodríguez-Gómez, 2011;Ornelas et al, 2013;Venkatraman et al, 2019;Rahbek et al, 2019). Species demographic dynamics of the TMCF in response to the climatic oscillations of the Pleistocene in the Neotropics have been explained by two main precipitation models (reviewed in Ramírez-Barahona & Eguiarte, 2013).…”

Section: Introductionmentioning

confidence: 99%

Influence of Pleistocene climatic oscillations on the phylogeography and demographic history of endemic vulnerable trees (sectionMagnolia) of the Tropical Montane Cloud Forest in Mexico

Rico

León-Tapia

Zurita-Solís

et al. 2021

PeerJ

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The Tropical Montane Cloud Forest (TMCF) is a highly dynamic ecosystem that has undergone frequent spatial changes in response to the interglacial-glacial cycles of the Pleistocene. These climatic fluctuations between cold and warm cycles have led to species range shifts and contractions-expansions, resulting in complex patterns of genetic structure and lineage divergence in forest tree species. In this study, we sequenced four regions of the chloroplast DNA (trnT-trnL, trnK5-matk, rpl32-trnL, trnS-trnG) for 20 populations and 96 individuals to evaluate the phylogeography, historical demography, and paleodistributions of vulnerable endemic TMCF trees in Mexico: Magnolia pedrazae (north-region), M. schiedeana (central-region), and M. schiedeana population Oaxaca (south-region). Our data recovered 49 haplotypes that showed a significant phylogeographic structure in three regions: north, central, and south. Bayesian Phylogeographic and Ecological Clustering (BPEC) analysis also supported the divergence in three lineages and highlighted the role of environmental factors (temperature and precipitation) in genetic differentiation. Our historical demography analyses revealed demographic expansions predating the Last Interglacial (LIG, ~125,000 years ago), while Approximate Bayesian Computation (ABC) simulations equally supported two contrasting demographic scenarios. The BPEC and haplotype network analyses suggested that ancestral haplotypes were geographically found in central Veracruz. Our paleodistributions modeling showed evidence of range shifts and expansions-contractions from the LIG to the present, which suggested the complex evolutionary dynamics associated to the climatic oscillations of the Pleistocene. Habitat management of remnant forest fragments where large and genetically diverse populations occur in the three TMCF regions analyzed would be key for the conservation of these magnolia populations.

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Cloudy with a chance of speciation: integrative taxonomy reveals extraordinary divergence within a Mesoamerican cloud forest bird

Cited by 31 publications

References 67 publications

A simulation-based method for selecting calibration areas for ecological niche models and species distribution models

A simulation-based method for selecting calibration areas for ecological niche models and species distribution models

Molecular Species Delimitation of Larks (Aves: Alaudidae), and Integrative Taxonomy of the Genus Calandrella, with the Description of a Range-Restricted African Relic Taxon

Influence of Pleistocene climatic oscillations on the phylogeography and demographic history of endemic vulnerable trees (sectionMagnolia) of the Tropical Montane Cloud Forest in Mexico

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