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Article ; Online: ASSESSING THE RELATIONSHIP BETWEEN SPECIATION AND EVOLUTIONARY CHANGE.

Mindell, David P / Sites, Jack W / Graur, Dan

Cladistics : the international journal of the Willi Hennig Society

2021 Volume 6, Issue 4, Page(s) 393–398

Language	English
Publishing date	2021-12-21
Publishing country	United States
Document type	Letter
ZDB-ID	1462608-1
ISSN	1096-0031 ; 0748-3007
ISSN (online)	1096-0031
ISSN	0748-3007
DOI	10.1111/j.1096-0031.1990.tb00555.x
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Article ; Online: Speciational Evolution: a Phylogenetic Test With Allozymes in Sceloporus (Reptilia).

Mindell, David P / Sites, Jack W / Graur, Dan

Cladistics : the international journal of the Willi Hennig Society

2021 Volume 5, Issue 1, Page(s) 49–61

Abstract: Abstract- The potential role of speciation in accelerating evolutionary divergence remains controversial. Earlier tests based on genetic and morphologic distances which indicated an absence of speciational evolution rely on problematic assumptions. We ... ...

Abstract	Abstract- The potential role of speciation in accelerating evolutionary divergence remains controversial. Earlier tests based on genetic and morphologic distances which indicated an absence of speciational evolution rely on problematic assumptions. We provide a phylogenetic test in which amounts of discrete character change relative to an outgroup are compared between sister taxa. Although this test is constrained by a need to assume similar extinction rates in groups compared, it provides conceptual improvements regarding monophyly, equal age of taxa, and distribution of homoplasy. Based on analysis of 68 informative allozyme characters for 19 lizard species in the genus Sceloporus, significant speciational evolution and punctuational change is, at least, a viable explanation for the distribution of observed character changes.
Language	English
Publishing date	2021-12-21
Publishing country	United States
Document type	Journal Article
ZDB-ID	1462608-1
ISSN	1096-0031 ; 0748-3007
ISSN (online)	1096-0031
ISSN	0748-3007
DOI	10.1111/j.1096-0031.1989.tb00482.x
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Article ; Online: Extinction, reintroduction, and restoration of a lizard meta-population equilibrium in the Missouri Ozarks.

Sites, Jack W

Molecular ecology

2013 Volume 22, Issue 14, Page(s) 3653–3655

Abstract: In this issue of Molecular Ecology, Neuwald & Templeton (2013) report on a 22-year study of natural populations of Collared Lizards (Crotaphytus collaris) that evolved on isolated on rock outcrops (‘glades’) in the Ozark Mountains in eastern Missouri. ... ...

Abstract	In this issue of Molecular Ecology, Neuwald & Templeton (2013) report on a 22-year study of natural populations of Collared Lizards (Crotaphytus collaris) that evolved on isolated on rock outcrops (‘glades’) in the Ozark Mountains in eastern Missouri. This ecosystem was originally maintained by frequent fires that kept the forest understory open, but fire-suppression was adopted as official policy in about 1945, which led to a loss of native biodiversity, including local extinctions of some lizard populations. Policies aimed at restoring biodiversity included controlled burns and re-introductions of lizards to some glades, which began in 1984. Populations were monitored from 1984–2006, and demographic and genetic data collected from 1 679 lizards were used to documents shifts in meta-population dynamics over four distinct phases of lizard recovery: 1–an initial translocation of lizards drawn from the same source populations onto three glades that were likely part of one metapopulation; 2–a period of isolation and genetic drift associated with the absence of fires; 3–a period of rapid colonization and population increase following restoration of fire; and 4–stabilization of the meta-population under regular prescribed burning. This study system thus provides a rare opportunity to characterize the dynamics of a landscape-scale management strategy on the restoration of the meta-population of a reintroduced species; long-term case studies of the extinction, founding, increase, and stabilization of a well-defined meta-population, based on both demographic and population genetic data, are rare in the conservation, ecological, and evolutionary literature.
MeSH term(s)	Animals ; Fires ; Genetic Variation ; Lizards/genetics
Language	English
Publishing date	2013-08-05
Publishing country	England
Document type	Journal Article ; Comment
ZDB-ID	1126687-9
ISSN	1365-294X ; 0962-1083
ISSN (online)	1365-294X
ISSN	0962-1083
DOI	10.1111/mec.12357
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Article ; Online: An integrative approach to address species limits in the southernmost members of the Liolaemus kingii group (Squamata: Liolaemini).

Sánchez, Kevin I / Avila, Luciano J / Sites, Jack W / Morando, Mariana

Molecular phylogenetics and evolution

2021 Volume 157, Page(s) 107046

Abstract: Recent conceptual and methodological advances have enabled an increasing number of studies to address the problem of species delimitation in a comprehensive manner. This is of particular interest in cases of species whose divergence times are recent and/ ... ...

Abstract	Recent conceptual and methodological advances have enabled an increasing number of studies to address the problem of species delimitation in a comprehensive manner. This is of particular interest in cases of species whose divergence times are recent and/or effective population sizes are large, where the conclusions obtained from a single source of evidence may lead to erroneous estimations of true species numbers or incorrect assignment of individuals to species. Iguanian lizards of the Liolaemus kingii group (13 species) comprise an important component of the endemic fauna of Patagonia. The southernmost species of this group (namely L. baguali, L. escarchadosi, L. sarmientoi, and L. tari) show widely overlapping distributions across southern Patagonia, also, their phylogenetic relationships are ambiguous and species boundaries have not been explicitly tested. Here we use a comprehensive approach to assess species limits through the use of molecular and morphological information (mitochondrial cytb, nuclear sequences collected by ddRADseq, and linear, meristic and landmark-based morphometrics). We found support for the current taxonomy given that the different analyses recognized the nominal species (4 entities), also a candidate species was supported by mitochondrial and morphological data. In addition, we detected signs of admixture between some of the species. Our results indicate that the L. kingii group can serve as a model system in studies of diversification accompanied by hybridization in nature, which in turn might have been promoted by past climatic oscillations and generalist morphologies. We emphasize the importance of using multiple lines of evidence in order to solve evolutionary stories, and minimizing potential erroneous results that may arise when relying on a single source of information.
MeSH term(s)	Analysis of Variance ; Animals ; Cytochromes b/genetics ; DNA, Mitochondrial ; Genetic Loci ; Geography ; Hybridization, Genetic ; Lizards/anatomy & histology ; Lizards/classification ; Lizards/genetics ; Phylogeny ; Polymorphism, Single Nucleotide/genetics ; Principal Component Analysis ; Species Specificity
Chemical Substances	DNA, Mitochondrial ; Cytochromes b (9035-37-4)
Language	English
Publishing date	2021-01-07
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	33610-5
ISSN	1095-9513 ; 1055-7903
ISSN (online)	1095-9513
ISSN	1055-7903
DOI	10.1016/j.ympev.2020.107046
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Article: Environmental correlates of phenotypic evolution in ecologically diverse

Edwards, Danielle L / Avila, Luciano J / Martinez, Lorena / Sites, Jack W / Morando, Mariana

Ecology and evolution

2022 Volume 12, Issue 6, Page(s) e9009

Abstract: Evolutionary correlations between phenotypic and environmental traits characterize adaptive radiations. However, the lizard ... ...

Abstract	Evolutionary correlations between phenotypic and environmental traits characterize adaptive radiations. However, the lizard genus
Language	English
Publishing date	2022-06-16
Publishing country	England
Document type	Journal Article
ZDB-ID	2635675-2
ISSN	2045-7758
ISSN	2045-7758
DOI	10.1002/ece3.9009
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Article ; Online: ExplorATE: a new pipeline to explore active transposable elements from RNA-seq data.

Femenias, Martin M / Santos, Juan C / Sites, Jack W / Avila, Luciano J / Morando, Mariana

Bioinformatics (Oxford, England)

2022 Volume 38, Issue 13, Page(s) 3361–3366

Abstract: Motivation: Transposable elements (TEs) are ubiquitous in genomes and many remain active. TEs comprise an important fraction of the transcriptomes with potential effects on the host genome, either by generating deleterious mutations or promoting ... ...

Abstract	Motivation: Transposable elements (TEs) are ubiquitous in genomes and many remain active. TEs comprise an important fraction of the transcriptomes with potential effects on the host genome, either by generating deleterious mutations or promoting evolutionary novelties. However, their functional study is limited by the difficulty in their identification and quantification, particularly in non-model organisms. Results: We developed a new pipeline [explore active transposable elements (ExplorATE)] implemented in R and bash that allows the quantification of active TEs in both model and non-model organisms. ExplorATE creates TE-specific indexes and uses the Selective Alignment (SA) to filter out co-transcribed transposons within genes based on alignment scores. Moreover, our software incorporates a Wicker-like criteria to refine a set of target TEs and avoid spurious mapping. Based on simulated and real data, we show that the SA strategy adopted by ExplorATE achieved better estimates of non-co-transcribed elements than other available alignment-based or mapping-based software. ExplorATE results showed high congruence with alignment-based tools with and without a reference genome, yet ExplorATE required less execution time. Likewise, ExplorATE expands and complements most previous TE analyses by incorporating the co-transcription and multi-mapping effects during quantification, and provides a seamless integration with other downstream tools within the R environment. Availability and implementation: Source code is available at https://github.com/FemeniasM/ExplorATEproject and https://github.com/FemeniasM/ExplorATE_shell_script. Data available on request. Supplementary information: Supplementary data are available at Bioinformatics online.
MeSH term(s)	DNA Transposable Elements ; RNA-Seq ; Software ; Exome Sequencing ; Transcriptome
Chemical Substances	DNA Transposable Elements
Language	English
Publishing date	2022-06-04
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1422668-6
ISSN	1367-4811 ; 1367-4803
ISSN (online)	1367-4811
ISSN	1367-4803
DOI	10.1093/bioinformatics/btac354
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Article ; Online: Complex Patterns of Diversification in the Gray Zone of Speciation: Model-Based Approaches Applied to Patagonian Liolaemid Lizards (Squamata: Liolaemus kingii clade).

Sánchez, Kevin I / Diaz Huesa, Emilce G / Breitman, María F / Avila, Luciano J / Sites, Jack W / Morando, Mariana

Systematic biology

2023 Volume 72, Issue 4, Page(s) 739–752

Abstract: In this study we detangled the evolutionary history of the Patagonian lizard clade Liolaemus kingii, coupling dense geographic sampling and novel computational analytical approaches. We analyzed nuclear and mitochondrial data (restriction site-associated ...

Abstract	In this study we detangled the evolutionary history of the Patagonian lizard clade Liolaemus kingii, coupling dense geographic sampling and novel computational analytical approaches. We analyzed nuclear and mitochondrial data (restriction site-associated DNA sequencing and cytochrome b) to hypothesize and evaluate species limits, phylogenetic relationships, and demographic histories. We complemented these analyses with posterior predictive simulations to assess the fit of the genomic data to the multispecies coalescent model. We also employed a novel approach to time-calibrate a phylogenetic network. Our results show several instances of mito-nuclear discordance and consistent support for a reticulated history, supporting the view that the complex evolutionary history of the kingii clade is characterized by extensive gene flow and rapid diversification events. We discuss our findings in the contexts of the "gray zone" of speciation, phylogeographic patterns in the Patagonian region, and taxonomic outcomes. [Model adequacy; multispecies coalescent; multispecies network coalescent; phylogenomics; species delimitation.].
MeSH term(s)	Lizards/classification ; Lizards/genetics ; Animals ; Phylogeny ; Cytochrome b Group/genetics ; Genotype ; Gene Flow ; Phylogeography/methods
Chemical Substances	Cytochrome b Group
Language	English
Publishing date	2023-04-11
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1482572-7
ISSN	1076-836X ; 1063-5157
ISSN (online)	1076-836X
ISSN	1063-5157
DOI	10.1093/sysbio/syad019
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Article: How important is it to consider lineage diversification heterogeneity in macroevolutionary studies? Lessons from the lizard family Liolaemidae

Olave, Melisa / Avila, Luciano J / Sites, Jack W / Morando, Mariana

Journal of biogeography. 2020 June, v. 47, no. 6

2020

Abstract: Macroevolutionary and biogeographical studies commonly apply multiple models to test state‐dependent diversification. These models track the association between states of interest along a phylogeny, although many of them do not consider whether different ...

Abstract	Macroevolutionary and biogeographical studies commonly apply multiple models to test state‐dependent diversification. These models track the association between states of interest along a phylogeny, although many of them do not consider whether different clades might be evolving under different evolutionary drivers. Yet, they are still commonly applied to empirical studies without careful consideration of possible lineage diversification heterogeneity along the phylogenetic tree. A recent biogeographic study has suggested that orogenic uplift of the southern Andes has acted as a species pump, driving diversification of the lizard family Liolaemidae (307 described species), native to temperate southern South America. Here, we argue against the Andean uplift as main driver of evolution in this group. We show that there is a clear pattern of heterogeneous diversification in the Liolaemidae, which biases state‐ and environment‐dependent analyses in, respectively, the GeoSSE and RPANDA programs. We show here that there are two shifts to accelerated speciation rates involving two clades that have both been classified as having “Andean” distributions. We incorporated the Geographic Hidden‐State Speciation and Extinction model (GeoHiSSE) to accommodate unrelated diversification shifts, and also re‐analyzed the data in RPANDA program after splitting biologically distinct clades for separate analyses, as well as including a more appropriate set of models. We demonstrate that the “Andean uplift” hypothesis is not supported when the heterogeneous diversification histories among these lizards is considered. We use the Liolaemidae as an ideal system to demonstrate potential risks of ignoring clade‐specific differences in diversification patterns in macroevolutionary studies. We also implemented simulations to show that, in agreement with previous findings, the HiSSE approach can effectively and substantially reduce the level of distribution‐dependent models receiving the highest AIC weights in such scenarios. However, we still find a relatively high rate (15%) of distribution‐dependent models receiving the highest AIC weights, and provide recommendations related to the set of models included in the analyses that reduce these rates by half. Finally, we demonstrate that trees including clades following different dependent‐drivers affect RPANDA analyses by producing different outcomes, ranging from partially correct models to completely misleading results. We provide recommendations for the implementation of both programs.
Keywords	biogeography ; extinction ; geographical distribution ; lizards ; models ; phylogeny ; Andes region ; South America
Language	English
Dates of publication	2020-06
Size	p. 1286-1297.
Publishing place	John Wiley & Sons, Ltd
Document type	Article
Note	NAL-AP-2-clean ; JOURNAL ARTICLE
ZDB-ID	188963-1
ISSN	0305-0270
ISSN	0305-0270
DOI	10.1111/jbi.13807
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: The enigmatic Leiosaurae clade: Phylogeography, species delimitation, phylogeny and historical biogeography of its southernmost species.

Femenias, Martin M / Avila, Luciano J / Sites, Jack W / Morando, Mariana

Molecular phylogenetics and evolution

2019 Volume 144, Page(s) 106725

Abstract: The clade Leiosaurae is composed of poorly-known species endemic to the southern region of South America. The difficulties of finding these lizards in the field, and their highly conserved morphology, have limited our taxonomic knowledge and ... ...

Abstract	The clade Leiosaurae is composed of poorly-known species endemic to the southern region of South America. The difficulties of finding these lizards in the field, and their highly conserved morphology, have limited our taxonomic knowledge and understanding of their evolutionary histories. Here, we use data collected over 9 years to study the phylogenetic history, genetic diversity, and biogeographic history of almost all the southernmost species of Leiosaurae (except P. nigroigulus), including: Leiosaurus bellii, Diplolaemus darwinii, D. bibronii, D. sexcinctus and D. leopardinus. We use a fragment of the mitochondrial cytochrome-b gene to resolve general phylogeographic patterns, and add another mitochondrial gene and eight nuclear genes to perform species delimitation and phylogenetic analyses associated with divergence times. We found evidence for three putative new species-level taxa within L. bellii and five within Diplolaemus species, indicating high levels of geographic structure. We use a time-calibrated phylogeny to estimate ranges of ancestral distributions and to generate new hypotheses about their historical biogeography.
MeSH term(s)	Animals ; Biological Evolution ; DNA, Mitochondrial/analysis ; DNA, Mitochondrial/genetics ; Ecosystem ; Genes, Mitochondrial ; Genetic Speciation ; Lizards/classification ; Lizards/genetics ; Phylogeny ; Phylogeography ; South America
Chemical Substances	DNA, Mitochondrial
Language	English
Publishing date	2019-12-26
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	33610-5
ISSN	1095-9513 ; 1055-7903
ISSN (online)	1095-9513
ISSN	1055-7903
DOI	10.1016/j.ympev.2019.106725
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Article: Phylogeographic analysis and species distribution modelling of the wood frog

Nuñez, José J / Suárez-Villota, Elkin Y / Quercia, Camila A / Olivares, Angel P / Sites, Jack W

PeerJ

2020 Volume 8, Page(s) e9980

Abstract: Background: The evolutionary history of southern South American organisms has been strongly influenced by Pleistocene climate oscillations. Amphibians are good models to evaluate hypotheses about the influence of these climate cycles on population ... ...

Abstract	Background: The evolutionary history of southern South American organisms has been strongly influenced by Pleistocene climate oscillations. Amphibians are good models to evaluate hypotheses about the influence of these climate cycles on population structure and diversification of the biota, because they are sensitive to environmental changes and have restricted dispersal capabilities. We test hypotheses regarding putative forest refugia and expansion events associated with past climatic changes in the wood frog Methods: Using three mitochondrial regions ( Results: Population structure and genealogical analyses support the existence of four lineages distributed north to south, with moderate to high phylogenetic support (Bootstrap > 70%; BPP > 0.92). The diversification time of
Language	English
Publishing date	2020-10-06
Publishing country	United States
Document type	Journal Article
ZDB-ID	2703241-3
ISSN	2167-8359
ISSN	2167-8359
DOI	10.7717/peerj.9980
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