Phylogenetic evidence of historic mitochondrial introgression and cryptic diversity in the genus Pseudemoia (Squamata: Scincidae)

Haines, Margaret L.; Moussalli, Adnan; Stuart‐Fox, Devi; Clemann, Nick; Melville, Jane

doi:10.1016/j.ympev.2014.09.006

Cited by 8 publications

(27 citation statements)

References 58 publications

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“…We interpret the rarity of the complex placenta amongst squamates as evidence that it is evolutionarily ‘difficult’, and thus it is exceedingly unlikely that the morphological and physiological changes associated with complex placentation evolve independently in the same genus. The positioning of B. duperreyi within Pseudemoia is incongruent with recent phylogenies of these taxa (Brandley et al, in press; Haines et al, ), and therefore an example of how phylogenetic error may result in provocative but erroneous, conclusions.…”

Section: Phylogenetic Accuracymentioning

confidence: 96%

Ancestral state reconstructions require biological evidence to test evolutionary hypotheses: A case study examining the evolution of reproductive mode in squamate reptiles

et al. 2015

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To understand evolutionary transformations it is necessary to identify the character states of extinct ancestors. Ancestral character state reconstruction is inherently difficult because it requires an accurate phylogeny, character state data, and a statistical model of transition rates and is fundamentally constrained by missing data such as extinct taxa. We argue that model based ancestral character state reconstruction should be used to generate hypotheses but should not be considered an analytical endpoint. Using the evolution of viviparity and reversals to oviparity in squamates as a case study, we show how anatomical, physiological, and ecological data can be used to evaluate hypotheses about evolutionary transitions. The evolution of squamate viviparity requires changes to the timing of reproductive events and the successive loss of features responsible for building an eggshell. A reversal to oviparity requires that those lost traits re-evolve. We argue that the re-evolution of oviparity is inherently more difficult than the reverse. We outline how the inviability of intermediate phenotypes might present physiological barriers to reversals from viviparity to oviparity. Finally, we show that ecological data supports an oviparous ancestral state for squamates and multiple transitions to viviparity. In summary, we conclude that the first squamates were oviparous, that frequent transitions to viviparity have occurred, and that reversals to oviparity in viviparous lineages either have not occurred or are exceedingly rare. As this evidence supports conclusions that differ from previous ancestral state reconstructions, our paper highlights the importance of incorporating biological evidence to evaluate model-generated hypotheses.

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Section: Phylogenetic Accuracymentioning

confidence: 96%

Ancestral state reconstructions require biological evidence to test evolutionary hypotheses: A case study examining the evolution of reproductive mode in squamate reptiles

et al. 2015

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“…2). Shrinking islands of high-altitude habitat across eastern Australia also continue to reveal previously unrecognised endemic lineages and taxa (Bell et al 2010;Hoskin and Couper 2014;Haines et al 2014). Finally, and perhaps most strikingly, recent work across the Australian Monsoonal Tropics has revealed an exceptional number of apparently restricted lineages that still await proper taxonomic assessment (Fujita et al 2010;Pepper et al 2011b;Smith et al 2011;Oliver et al 2012Oliver et al , 2014bMarin et al 2013;Rabosky et al 2014a).…”

Section: Australian Reptiles As a Case Studymentioning

confidence: 98%

“…Such introgression has been detected via multilocus studies in several Australian reptiles (Rabosky et al 2009;Haines et al 2014) and amphibians (Catullo and Keogh 2014), and has even occurred in human evolution, where regional populations of modern Homo sapiens show evidence of introgression from other differentiated hominid lineages -the Denisovians and Neanderthals (Reich et al 2011;Yang et al 2012). This poses important questions about how frequent gene flow is between lineages that otherwise show strong evidence of evolutionary divergence (i.e.…”

Section: Box 2 the Expanding Toolbox For Accessing Genome-scale Datamentioning

confidence: 99%

New approaches to cataloguing and understanding evolutionary diversity: a perspective from Australian herpetology

2014

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Species are a fundamental unit for all fields of biology but conceptual and practical limitations have hampered the process of identifying and describing species in many organismal groups. One outcome of these challenges is the accumulation of genetically divergent lineages and morphologically distinctive populations that are 'known', but remain of uncertain taxonomic status and evolutionary significance. These lineages are also currently not effectively incorporated into evolutionary studies or conservation planning and management. Here we suggest three ways to address this issue. First, there is a need to develop improved frameworks to systematically capture taxonomically unrecognised lineage diversity. Second, increased utilisation of metadata frameworks will allow better recording and dissemination of biodiversity information. Finally, emerging genomic and analytical techniques will provide powerful new tools to improve our identification and understanding of evolutionary lineages.

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“…cryodroma plus P. entrecasteauxii occurred as late as 4 mya, with more recent divergence occurring between P. cryodroma and P. entrecasteauxii (Haines et al . ). We have previously provided evidence of historic hybridization between all three species pairs, with probable mitochondrial introgression from P. pagenstecheri into P. entrecasteauxii and P. cryodroma, as well as P. entrecasteauxii into its sister species P. cryodroma (Haines et al .…”

Section: Introductionmentioning

confidence: 97%

“…), we examine three species that exhibit genetic signatures of historical mitochondrial introgression (Haines et al . ) at three geographically isolated locations. All three species, P. cryodroma , P. entrecasteauxii and P. pagenstecheri , are morphologically similar and occupy overlapping ecological niches in the montane and subalpine regions (>1100 m above sea level) of southeastern Australia (Wilson & Swan ).…”

Section: Introductionmentioning

confidence: 99%

Geographic variation in hybridization and ecological differentiation between three syntopic, morphologically similar species of montane lizards

et al. 2016

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To understand factors shaping species boundaries in closely related taxa, a powerful approach is to compare levels of genetic admixture at multiple points of contact and determine how this relates to intrinsic and extrinsic factors, such as genetic, morphological and ecological differentiation. In the Australian Alps, the threatened alpine bog skink Pseudemoia cryodroma co-occurs with two morphologically and ecologically similar congeners, P. entrecasteauxii and P. pagenstecheri, and all three species are suspected to hybridize. We predicted that the frequency of hybridization should be negatively correlated with genetic divergence, morphological differentiation and microhabitat separation. We tested this hypothesis using a mitochondrial locus, 13 microsatellite loci, morphological and microhabitat data and compared results across three geographically isolated sites. Despite strong genetic structure between species, we detected hybridization between all species pairs, including evidence of backcrossed individuals at the two sites where all three species are syntopic. Hybridization frequencies were not consistently associated with genetic, morphological or ecological differentiation. Furthermore, P. entrecasteauxii and P. pagenstecheri only hybridized at the two sites where they are syntopic with P. cryodroma, but not at the largest site where P. cryodroma was not recorded, suggesting that P. cryodroma may serve as a bridging species. This study reveals the complex dynamics within a three species hybrid zone and provides a baseline for assessing the impact of climate change and anthropogenic habitat modification on future hybridization frequencies.

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Phylogenetic evidence of historic mitochondrial introgression and cryptic diversity in the genus Pseudemoia (Squamata: Scincidae)

Cited by 8 publications

References 58 publications

Ancestral state reconstructions require biological evidence to test evolutionary hypotheses: A case study examining the evolution of reproductive mode in squamate reptiles

Ancestral state reconstructions require biological evidence to test evolutionary hypotheses: A case study examining the evolution of reproductive mode in squamate reptiles

New approaches to cataloguing and understanding evolutionary diversity: a perspective from Australian herpetology

Geographic variation in hybridization and ecological differentiation between three syntopic, morphologically similar species of montane lizards

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