Next-generation sequencing reveals phylogeographic structure and a species tree for recent bird divergences

McCormack, John E.; Maley, James M.; Hird, Sarah M.; Derryberry, Elizabeth P.; Graves, Gary R.; Brumfield, Robb T.

doi:10.1016/j.ympev.2011.10.012

Cited by 88 publications

(70 citation statements)

References 53 publications

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“…Highthroughput sequencing methods are already facilitating the collection of multi-locus datasets for large numbers of individuals (McCormack et al, 2012). These technologies also offer perspectives for sampling new types of informative markers.…”

Section: Future Perspectivesmentioning

confidence: 99%

DNA-based species delimitation in algae

Leliaert

Verbruggen

Vanormelingen

et al. 2014

European Journal of Phycology

309

285

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Given the problems of species delimitation in algae using morphology or sexual compatibility, molecular data are becoming the standard for delimiting species and testing their traditional boundaries. The idea that species are separately evolving metapopulation lineages, along with theoretical progress in phylogenetic and population genetic analyses, has led to the development of new methods of species delimitation. We review these recent developments in DNA-based species delimitation methods, and discuss how they have changed and continue to change our understanding of algal species boundaries. Although single-locus approaches have proven effective for a first rapid and large-scale assessment of species diversity, species delimitation based on single gene trees falls short due to gene tree-species tree incongruence, caused by confounding processes like incomplete lineage sorting, trans-species polymorphism, hybridization and introgression. Data from unlinked loci and multi-species coalescent methods, which combine principles from phylogenetics and population genetics, may now be able to account for these complicating factors. Several of these methods also provide statistical support regarding species boundaries, which is important because speciation is a process and therefore uncertainty about precise species boundaries is inevitable in recently diverged lineages.

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Section: Future Perspectivesmentioning

confidence: 99%

DNA-based species delimitation in algae

Leliaert

Verbruggen

Vanormelingen

et al. 2014

European Journal of Phycology

309

285

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“…Phenotypic differences can arise quickly through localized divergent selection, or, alternatively, they may seem to arise quickly because traditional molecular markers may not detect the phylogenetic structure underlying rapid diversification (47). Dark-eyed juncos, for example, exhibit pronounced phenotypic variation that is geographically clustered among subspecies that exhibit little to no phylogeographic structure (48). This pattern likely reflects subtle phylogeographic structure resulting from recent, rapid genetic isolation or adaptive divergence with ongoing gene flow among subspecies.…”

Section: Geographically Clustered Phenotypes Without Phylogeographicmentioning

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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“…Individuals from different populations, or even from the same, can be compared to find regions of diversity within their genome that can be used as markers to undertake population genetic, phylogeographic or phylogenetic analyses by designing highly specific primers. An alternative strategy is to use NGS to simultaneously obtain genomic information for all the individuals under study, as in [50]. In the case of Tricladida, these strategies are in their infancy, some complete mitochondrial genomes have already been published [51] and others are on the way (non-published data).…”

Section: Weaknesses Of Molecular Markers and Future Studiesmentioning

confidence: 99%

Planarian (Platyhelminthes, Tricladida) Diversity and Molecular Markers: A New View of an Old Group

Álvarez‐Presas

Riutort

2014

Diversity

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Planarians are a group of free-living platyhelminths (triclads) best-known largely due to long-standing regeneration and pattern formation research. However, the group's diversity and evolutionary history has been mostly overlooked. A few taxonomists have focused on certain groups, resulting in the description of many species and the establishment of higher-level groups within the Tricladida. However, the scarcity of morphological features precludes inference of phylogenetic relationships among these taxa. The incorporation of molecular markers to study their diversity and phylogenetic relationships has facilitated disentangling many conundrums related to planarians and even allowed their use as phylogeographic model organisms. Here, we present some case examples ranging from delimiting species in an integrative style, and barcoding them, to analysing their evolutionary history on a lower scale to infer processes affecting biodiversity origin, or on a higher scale to understand the genus level or even higher relationships. In many cases, these studies have allowed proposing better classifications and resulted in taxonomical changes. We also explain shortcomings resulting in a lack of resolution or power to apply the most up-to-date data analyses. Next-generation sequencing methodologies may help improve this situation and accelerate their use as model organisms.

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Next-generation sequencing reveals phylogeographic structure and a species tree for recent bird divergences

Cited by 88 publications

References 53 publications

DNA-based species delimitation in algae

DNA-based species delimitation in algae

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

Planarian (Platyhelminthes, Tricladida) Diversity and Molecular Markers: A New View of an Old Group

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