Toward an organismal, integrative, and iterative phylogeography

Buckley, David

doi:10.1002/bies.200800162

Cited by 39 publications

(28 citation statements)

References 76 publications

(99 reference statements)

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“…type of habitat, climatic variables, etc.) with an important role in understanding the biology and natural history of organisms (Buckley 2009) and large-scale biogeographic patterns (Wiens 2011). Recently, several studies have initiated this approach, linking ecological niche modelling with phylogeographic analysis in an attempt to answer questions related to evolutionary processes within sister species or intraspecific lineages (Graham et al 2004;Jakob et al 2007;Gallego and Galián 2008;McCormack et al 2010;Hundsdoerfer et al 2011;Pearman et al 2010;Oney et al 2013;Schulte et al 2012).…”

Section: Introductionmentioning

confidence: 99%

Distribution of Tomicus destruens (Coleoptera: Scolytinae) mitochondrial lineages: phylogeographic insights and niche modelling

2014

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This paper presents a novel approach of population genetics together with environmental and biogeographic data leading to inferences for ecological niche modelling. We used hierarchical lineages obtained using the nested cladistic analysis (NCA) of the mitochondrial DNA (mtDNA) haplotypes of the bark beetle species Tomicus destruens, for modelling the distribution by maximum entropy using environmental and host variables along the whole Mediterranean Basin. The identity and similarity tests were checked in the intraspecific lineages (NCA clades and haplotypes) in order to determine a shift or conservatism niche between them. Also, four indices from nine geographical areas in the Mediterranean Basin were calculated to assess the variability of environmental factors shaping the distribution of haplotype diversity on a large geographic scale. The ecological models developed indicate that minority eastern mtDNA lineages of T. destruens differ in their potential ecological niche according to their relation to extreme climatic variables. By contrast, the most widespread western lineages display a close relationship with their Pinus host tree. Also, higher levels of exclusive and endemic haplotypes were predicted in areas with high temperature variability in the Mediterranean wet period. The eastern group niche seems to be included in part of the range of the ecological space of the two major western clades. This result suggests that a niche shift might have started, being still an early relationship with its host tree Pinus brutia. Alternatively, the temperature variability in the wettest period appears to be related to a high proportion of endemic haplotypes of T. destruens, possibly by involving a balance between the length of the flight reproductive period of T. destruens and the status of the host tree vigour and growth stage. This study illustrates a good example of the benefits that ecological niche modelling provides to understand population genetic and phylogeographic patterns.

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Section: Introductionmentioning

confidence: 99%

Distribution of Tomicus destruens (Coleoptera: Scolytinae) mitochondrial lineages: phylogeographic insights and niche modelling

2014

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“…Our specific goals here are to: (i) provide a well‐resolved, time‐calibrated phylogenetic/phylogeographic hypothesis for the lineomaculatus group and to assess clade and lineage origins within the historical Miocene‐to‐Pleistocene events of southern Patagonia; and (ii) qualitatively evaluate geographic concordance of refugia and phylogeographic breaks inferred from these lizards, with those proposed for plants and rodents in the same region. Because both phylogeography and species delimitation are integrative and iterative fields of study (Buckley ; Padial et al . ), this research will contribute to a foundation upon which future studies, based on additional data for these lizards and studies of codistributed species, will further clarify phylogenetic and speciation histories in this region.…”

Section: Introductionmentioning

confidence: 99%

How lizards survived blizzards: phylogeography of theLiolaemus lineomaculatusgroup (Liolaemidae) reveals multiple breaks and refugia in southernPatagonia and their concordance with other codistributed taxa

et al. 2012

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Patagonia was shaped by a complex geological history, including the Miocene uplift of the Andes, followed by volcanism, marine introgressions, and extreme climatic oscillations during Pliocene-Pleistocene glaciation-deglaciation cycles. The distributional patterns and phylogenetic relationships of southern patagonian animals and plants were affected in different ways, and those imprints are reflected in the seven phylogeographic breaks and eight refugia that have been previously proposed. In this study, we estimated time-calibrated phylogenetic/phylogeographic patterns in lizards of the Liolaemus lineomaculatus group and relate them to historical Miocene-to-Pleistocene events of Patagonia and the previously proposed phylogeographic patterns. Individuals from 51 localities were sequenced for the mitochondrial marker (cyt-b) and a subsample of individuals from each mitochondrial lineage was sequenced for one nuclear (LDA12D) and one slow evolving mitochondrial gene (12S). Our analyses revealed strong phylogeographic structure among lineages and, in most cases, no signal of demographic changes through time. The lineomaculatus group is composed of three strongly supported clades (lineomaculatus, hatcheri and kolengh + silvanae), and divergence estimates suggested their origins associated with the oldest known Patagonian glaciation (7-5 Ma); subsequent diversification within the lineomaculatus clade coincided with the large Pliocene glaciations (~3.5 Ma). The lineomaculatus clade includes nine strongly genetically and geographically structured lineages, five of which are interpreted as candidate species. Our findings suggest that some Liolaemus lineages have persisted in situ, each of them in a different refugium, through several glaciation-deglaciation cycles without demographic fluctuations. We also summarize and update qualitative evidence of some shared phylogeographic breaks and refugia among plants, rodents and lizards.

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“…This analytical framework bridged microevolutionary processes acting within populations and macroevolutionary patterns at larger spatial and temporal scales. From the earliest applications, empirical phylogeographic studies described spatial patterns of genetic diversity and inferred underlying mechanisms, thus contributing to the explanatory and predictive power of the field (2). If most species show phylogeographic structure caused by landscape features that impede gene flow, then the geographic distribution of divergent lineages should coincide among species that coinhabit those landscapes.…”

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confidence: 99%

Phenotypes in phylogeography: Species’ traits, environmental variation, and vertebrate diversification

Zamudio

Bell

Mason

2016

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

199

175

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Almost 30 y ago, the field of intraspecific phylogeography laid the foundation for spatially explicit and genealogically informed studies of population divergence. With new methods and markers, the focus in phylogeography shifted to previously unrecognized geographic genetic variation, thus reducing the attention paid to phenotypic variation in those same diverging lineages. Although phenotypic differences among lineages once provided the main data for studies of evolutionary change, the mechanisms shaping phenotypic differentiation and their integration with intraspecific genetic structure have been underexplored in phylogeographic studies. However, phenotypes are targets of selection and play important roles in species performance, recognition, and diversification. Here, we focus on three questions. First, how can phenotypes elucidate mechanisms underlying concordant or idiosyncratic responses of vertebrate species evolving in shared landscapes? Second, what mechanisms underlie the concordance or discordance of phenotypic and phylogeographic differentiation? Third, how can phylogeography contribute to our understanding of functional phenotypic evolution? We demonstrate that the integration of phenotypic data extends the reach of phylogeography to explain the origin and maintenance of biodiversity. Finally, we stress the importance of natural history collections as sources of high-quality phenotypic data that span temporal and spatial axes.phylogeography | phenotype | function | trait | concordance P hylogeography, as originally defined, focused on processes governing the spatial distribution of genealogical lineages within species (1). One of the strengths of the field at its inception was formalizing conceptual links among heredity (processes at the level of individual pedigrees), divergence at the population level, and phylogenetic relationships among species (1). This analytical framework bridged microevolutionary processes acting within populations and macroevolutionary patterns at larger spatial and temporal scales. From the earliest applications, empirical phylogeographic studies described spatial patterns of genetic diversity and inferred underlying mechanisms, thus contributing to the explanatory and predictive power of the field (2). If most species show phylogeographic structure caused by landscape features that impede gene flow, then the geographic distribution of divergent lineages should coincide among species that coinhabit those landscapes. Further, phylogeographic breaks or contact zones should arise as lineages diverge allopatrically or come into secondary contact after divergence, respectively. This explicit prediction (1) resulted in a search for shared geographic patterns in genetic structure among species and the birth of comparative phylogeography (3, 4). Now, with thousands of taxon-specific phylogeographic studies published and synthesized in comparative studies (5, 6), we have learned a tremendous amount about the geography of genetic structure both within and among species.Phylogeogra...

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Toward an organismal, integrative, and iterative phylogeography

Cited by 39 publications

References 76 publications

Distribution of Tomicus destruens (Coleoptera: Scolytinae) mitochondrial lineages: phylogeographic insights and niche modelling

Distribution of Tomicus destruens (Coleoptera: Scolytinae) mitochondrial lineages: phylogeographic insights and niche modelling

How lizards survived blizzards: phylogeography of theLiolaemus lineomaculatusgroup (Liolaemidae) reveals multiple breaks and refugia in southernPatagonia and their concordance with other codistributed taxa

Phenotypes in phylogeography: Species’ traits, environmental variation, and vertebrate diversification

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