Adding More Ecology into Species Delimitation: Ecological Niche Models and Phylogeography Help Define Cryptic Species in the Black Salamander (Aneides flavipunctatus)

Rissler, Leslie J.; Apodaca, Joseph J.

doi:10.1080/10635150701703063

Cited by 419 publications

(403 citation statements)

References 69 publications

Supporting

Mentioning

379

Contrasting

Unclassified

Order By: Relevance

“…genetic drift, mutations) or by divergent selection [2,25]. Longer periods of isolation are expected to increase ecological differentiation/divergence [26,27], and this has been demonstrated in several taxa [28,29].…”

Section: Introductionmentioning

confidence: 99%

Identifying cryptic diversity with predictive phylogeography

et al. 2016

View full text Add to dashboard Cite

Identifying units of biological diversity is a major goal of organismal biology. An increasing literature has focused on the importance of cryptic diversity, defined as the presence of deeply diverged lineages within a single species. While most discoveries of cryptic lineages proceed on a taxon-by-taxon basis, rapid assessments of biodiversity are needed to inform conservation policy and decision-making. Here, we introduce a predictive framework for phylogeography that allows rapidly identifying cryptic diversity. Our approach proceeds by collecting environmental, taxonomic and genetic data from codistributed taxa with known phylogeographic histories. We define these taxa as a reference set, and categorize them as either harbouring or lacking cryptic diversity. We then build a random forest classifier that allows us to predict which other taxa endemic to the same biome are likely to contain cryptic diversity. We apply this framework to data from two sets of disjunct ecosystems known to harbour taxa with cryptic diversity: the mesic temperate forests of the Pacific Northwest of North America and the arid lands of Southwestern North America. The predictive approach presented here is accurate, with prediction accuracies placed between 65% and 98.79% depending of the ecosystem. This seems to indicate that our method can be successfully used to address ecosystemlevel questions about cryptic diversity. Further, our application for the prediction of the cryptic/non-cryptic nature of unknown species is easily applicable and provides results that agree with recent discoveries from those systems. Our results demonstrate that the transition of phylogeography from a descriptive to a predictive discipline is possible and effective.

show abstract

Section: Introductionmentioning

confidence: 99%

Identifying cryptic diversity with predictive phylogeography

et al. 2016

View full text Add to dashboard Cite

show abstract

“…Most of the proposed species boundaries within the P. coronatum complex occur at junctions separating different ecological regions in Baja California (7), which implies that ecological diversification has played a critical role during lineage formation in this system. Ecological divergence represents an important stage during the process of lineage separation that has become increasingly feasible to quantify by using geographical information systems (GIS), and it is furthermore now possible to integrate these data within a phylogeographic framework (8)(9)(10). Predicting the geographic distributions of lineages can help to identify barriers to dispersal that are important because they can restrict gene flow and facilitate population divergence on an evolutionary timescale (11).…”

mentioning

confidence: 99%

Quantifying ecological, morphological, and genetic variation to delimit species in the coast horned lizard species complex ( Phrynosoma )

Leaché

Koo

Spencer

et al. 2009

Proc. Natl. Acad. Sci. U.S.A.

207

160

View full text Add to dashboard Cite

Lineage separation and divergence form a temporally extended process whereby populations may diverge genetically, morphologically, or ecologically, and these contingent properties of species provide the operational criteria necessary for species delimitation. We inferred the historical process of lineage formation in the coast horned lizard (Phrynosoma coronatum) species complex by evaluating a diversity of operational species criteria, including divergence in mtDNA (98 specimens; 2,781 bp) and nuclear loci (RAG؊1, 1,054 bp; BDNF 529 bp), ecological niches (11 bioclimatic variables; 285 unique localities), and cranial horn shapes (493 specimens; 16 landmarks). A phylogenetic analysis of mtDNA recovers 5 phylogeographic groups arranged latitudinally along the Baja California Peninsula and in California. The 2 southern phylogeographic groups exhibit concordance between genetic, morphological, and ecological divergence; however, differentiation is weak or absent at more recent levels defined by phylogeographic breaks in California. Interpreting these operational species criteria together suggests that there are 3 ecologically divergent and morphologically diagnosable species within the P. coronatum complex. Our 3-species taxonomic hypothesis invokes a deep coalescence event when fitting the mtDNA genealogy into the species tree, which is not unexpected for populations that have diverged recently. Although the hypothesis that the 3 phylogeographic groups distributed across California each represent distinctive species is not supported by all of the operational species criteria evaluated in this study, the conservation status of the imperiled populations represented by these genealogical units remains critical.evolution ͉ geometric morphometrics ͉ niche modeling ͉ phylogeography ͉ speciation

show abstract

“…31). In the Salamandridae, vicariant species formation appears to be the rule, as exemplified in many cases studies: (32)(33)(34)(35)(36). Nonadaptive species formation, fragmentation of an ancestral species range with niche conservation through time, was suggested to explain the ecological similarity of plethodontid salamanders in California (7).…”

Section: Evolution Of Niches and Geographic Ranges: Patterns Vs Procmentioning

confidence: 99%

“…Nonadaptive species formation, fragmentation of an ancestral species range with niche conservation through time, was suggested to explain the ecological similarity of plethodontid salamanders in California (7). Information on observed spatial patterns in relation to climate envelopes is increasingly used in studies of species formation (5,15,36). For example, comparisons of the distribution and environmental suitability between sister pairs of species of montane plethodontid salamanders suggested that niche conservatism may promote allopatric species formation (5).…”

Section: Evolution Of Niches and Geographic Ranges: Patterns Vs Procmentioning

confidence: 99%

Reconstruction of the climate envelopes of salamanders and their evolution through time

Vieites

Nieto-Román

Wake

2009

Proc. Natl. Acad. Sci. U.S.A.

View full text Add to dashboard Cite

Ecological niches evolve through time, but at different rates and to different degrees. An integrated approach using diverse databases, methods, and analytical tools is used to estimate climate envelopes for species of salamanders (family Salamandridae). These species, which range widely across the Holarctic and have a rich and long fossil record, are used to probe the evolutionary dynamics of niches studied in a phylogenetic context through time and across space. Climate data and statistical methods are used to estimate niche dimensions related to precipitation and temperature, in both a phylogenetic and ecogeographic context. Using phylogenetic methods, climate envelopes are estimated for segments of a time-calibrated phylogenetic tree of salamandrids, to explore how far back in time it is reasonable to make such estimates. Our research strategy illuminates some of the challenges and limitations of the available data and methods and identifies potential solutions, such as the need for physiological and behavioral data that may help to better define species' niches or the development of novel evolutionary models that account for paleoclimatic data. We explore and analyze limits to the application of currently available methodologies. Organisms known to have evolved slowly and conservatively, and which are ectotherms and likely to be profoundly affected by climatic variables, may be the most useful for studies of this kind.Grinnellian niches ͉ niche evolution ͉ phylogenetic analysis ͉ Salamandridae

show abstract

Adding More Ecology into Species Delimitation: Ecological Niche Models and Phylogeography Help Define Cryptic Species in the Black Salamander (Aneides flavipunctatus)

Cited by 419 publications

References 69 publications

Identifying cryptic diversity with predictive phylogeography

Identifying cryptic diversity with predictive phylogeography

Quantifying ecological, morphological, and genetic variation to delimit species in the coast horned lizard species complex ( Phrynosoma )

Reconstruction of the climate envelopes of salamanders and their evolution through time

Contact Info

Product

Resources

About