Phylogenetic Systematics and the Species Problem

Queiroz, Kevin de; Donoghue, Michael J.

doi:10.1111/j.1096-0031.1988.tb00518.x

Cited by 320 publications

(170 citation statements)

References 51 publications

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“…Nevertheless, serial homology and taxic homology are fundamentally different from the perspective of systematics, which is concerned with interorganismic hierarchical organization. Serial homology, an intraorganismic kind of order, is therefore outside the realm of most present-day systematics (but see de Queiroz and Donoghue, 1988, andNelson, 1989, for unorthodox views of inter-/intraorganismic approaches and their relation to taxa).…”

Section: Taxic and Transformational Homologymentioning

confidence: 99%

Concepts and Tests of Homology in the Cladistic Paradigm

1991

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Abstract-Logical equivalence between the notions of homology and synapomorphy is reviewed and supported. So-called transformational homology embodies two distinct logical components, one related to comparisons among different organisms and the other restricted to comparisons within the same organism. The former is essentially hierarchical in nature, thus being in fact a less obvious form of taxic homology. The latter is logically equivalent to so-called serial homology in a broad sense (including homonomy, mass homology or iterative homology) -Of three tests of homology proposed to date (similarity, conjunction and congruence) only congruence serves as a test in the strict sense. Similarity stands at a basic level in homology propositions, being the source of the homology conjecture in the first place. Conjunction is unquestionably an indicator of non-homology, but it is not specific about the pairwise comparison where non-homology is present, and depends on a specific scheme of relationship in order to refute a hypothesis of homology. The congruence test has been previously seen as an application of compatibility analysis-However, congruence is more appropriately seen as an expression of strict parsimony analysis. A general theoretical solution is proposed to determine evolution of characters with ambiguous distributions, based on the notion of maximization of . homology propositions. According to that notion, ambiguous character-state distributions should be resolved by an optimization that maximizes reversals relative to parallelisms. Notions of homology in morphology and molecular biology are essentially the same. The present tendency to adopt different terminologies for the two sources of data should be avoided, in order not to obscure the fundamental uniformity of the concept of homology in comparative biology.

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Section: Taxic and Transformational Homologymentioning

confidence: 99%

Concepts and Tests of Homology in the Cladistic Paradigm

1991

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“…To evaluate lineage divergence in light of the phylogenetic species concept (de Queiroz and Donoghue, 1988), pairwise …”

Section: Pairwise K-2p Distancesmentioning

confidence: 99%

The phylogeography of an alpine leaf beetle: Divergence within Oreina elongata spans several ice ages

Borer

Alvarez

Buerki

et al. 2010

Molecular Phylogenetics and Evolution

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a b s t r a c tThe genetic landscape of the European flora and fauna was shaped by the ebb and flow of populations with the shifting ice during Quaternary climate cycles. While this has been well demonstrated for lowland species, less is known about high altitude taxa. Here we analyze the phylogeography of the leaf beetle Oreina elongata from 20 populations across the Alps and Apennines. Three mitochondrial and one nuclear region were sequenced in 64 individuals. Within an mtDNA phylogeny, three of seven subspecies are monophyletic. The species is chemically defended and aposematic, with green and blue forms showing geographic variation and unexpected within-population polymorphism. These warning colors show pronounced east-west geographical structure in distribution, but the phylogeography suggests repeated origin and loss. Basal clades come from the central Alps. Ancestors of other clades probably survived across northern Italy and the northern Adriatic, before separation of eastern, southern and western populations and rapid spread through the western Alps. After reviewing calibrated gene-specific substitution rates in the literature, we use partitioned Bayesian coalescent analysis to date our phylogeography. The major clades diverged long before the last glacial maximum, suggesting that O. elongata persisted many glacial cycles within or at the edges of the Alps and Apennines. When analyzing additional barcoding pairwise distances, we find strong evidence to consider O. elongata as a species complex rather than a single species.

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“…In this case, the entire mainland species is no longer an exclusive group-it is paraphyletic with respect to the island population and loses its status as a GS at the moment that the island species becomes exclusive. As individuals in mainland populations are no longer members of any GS, some have suggested calling such groups ''metaspecies' ' (de Queiroz and Donoghue 1988).…”

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confidence: 99%

Mathematical Consequences of the Genealogical Species Concept

2002

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Abstract.A genealogical species is defined as a basal group of organisms whose members are all more closely related to each other than they are to any organisms outside the group (''exclusivity''), and which contains no exclusive group within it. In practice, a pair of species is so defined when phylogenies of alleles from a sample of loci shows them to be reciprocally monophyletic at all or some specified fraction of the loci. We investigate the length of time it takes to attain this status when an ancestral population divides into two descendant populations of equal size with no gene exchange, and when genetic drift and mutation are the only evolutionary forces operating. The number of loci used has a substantial effect on the probability of observing reciprocal monophyly at different times after population separation, with very long times needed to observe complete reciprocal monophyly for a large number of loci. In contrast, the number of alleles sampled per locus has a relatively small effect on the probability of reciprocal monophyly. Because a single mitochondrial or chloroplast locus becomes reciprocally monophyletic much faster than does a single nuclear locus, it is not advisable to use mitochondrial and chloroplast DNA to recognize genealogical species for long periods after population divergence. Using a weaker criterion of assigning genealogical species status when more than 50% of sampled nuclear loci show reciprocal monophyly, genealogical species status depends much less on the number of sampled loci, and is attained at roughly 4-7 N generations after populations are isolated, where N is the historically effective population size of each descendant. If genealogical species status is defined as more than 95% of sampled nuclear loci showing reciprocal monophyly, this status is attained after roughly 9-12 N generations.

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Phylogenetic Systematics and the Species Problem

Cited by 320 publications

References 51 publications

Concepts and Tests of Homology in the Cladistic Paradigm

Concepts and Tests of Homology in the Cladistic Paradigm

The phylogeography of an alpine leaf beetle: Divergence within Oreina elongata spans several ice ages

Mathematical Consequences of the Genealogical Species Concept

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