Dataset Information

Inferring species trees from gene trees in a radiation of California trapdoor spiders (Araneae, Antrodiaetidae, Aliatypus).

ABSTRACT:

Background

The California Floristic Province is a biodiversity hotspot, reflecting a complex geologic history, strong selective gradients, and a heterogeneous landscape. These factors have led to high endemic diversity across many lifeforms within this region, including the richest diversity of mygalomorph spiders (tarantulas, trapdoor spiders, and kin) in North America. The trapdoor spider genus Aliatypus encompasses twelve described species, eleven of which are endemic to California. Several Aliatypus species show disjunct distributional patterns in California (some are found on both sides of the vast Central Valley), and the genus as a whole occupies an impressive variety of habitats.

Methodology/principal findings

We collected specimens from 89 populations representing all described species. DNA sequence data were collected from seven gene regions, including two newly developed for spider systematics. Bayesian inference (in individual gene tree and species tree approaches) recovered a general "3 clade" structure for the genus (A. gulosus, californicus group, erebus group), with three other phylogenetically isolated species differing slightly in position across different phylogenetic analyses. Because of extremely high intraspecific divergences in mitochondrial COI sequences, the relatively slowly evolving 28S rRNA gene was found to be more useful than mitochondrial data for identification of morphologically indistinguishable immatures. For multiple species spanning the Central Valley, explicit hypothesis testing suggests a lack of monophyly for regional populations (e.g., western Coast Range populations). Phylogenetic evidence clearly shows that syntopy is restricted to distant phylogenetic relatives, consistent with ecological niche conservatism.

Conclusions/significance

This study provides fundamental insight into a radiation of trapdoor spiders found in the biodiversity hotspot of California. Species relationships are clarified and undescribed lineages are discovered, with more geographic sampling likely to lead to additional species diversity. These dispersal-limited taxa provide novel insight into the biogeography and Earth history processes of California.

SUBMITTER: Satler JD

PROVIDER: S-EPMC3180454 | biostudies-literature | 2011

REPOSITORIES: biostudies-literature

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Publications

Inferring species trees from gene trees in a radiation of California trapdoor spiders (Araneae, Antrodiaetidae, Aliatypus).

Satler Jordan D JD Starrett James J Hayashi Cheryl Y CY Hedin Marshal M

PloS one 20110926 9

<h4>Background</h4>The California Floristic Province is a biodiversity hotspot, reflecting a complex geologic history, strong selective gradients, and a heterogeneous landscape. These factors have led to high endemic diversity across many lifeforms within this region, including the richest diversity of mygalomorph spiders (tarantulas, trapdoor spiders, and kin) in North America. The trapdoor spider genus Aliatypus encompasses twelve described species, eleven of which are endemic to California. S ...[more]

PMID: 21966507

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Project description:BACKGROUND: Constructing species trees from multi-copy gene trees remains a challenging problem in phylogenetics. One difficulty is that the underlying genes can be incongruent due to evolutionary processes such as gene duplication and loss, deep coalescence, or lateral gene transfer. Gene tree estimation errors may further exacerbate the difficulties of species tree estimation. RESULTS: We present a new approach for inferring species trees from incongruent multi-copy gene trees that is based on a generalization of the Robinson-Foulds (RF) distance measure to multi-labeled trees (mul-trees). We prove that it is NP-hard to compute the RF distance between two mul-trees; however, it is easy to calculate this distance between a mul-tree and a singly-labeled species tree. Motivated by this, we formulate the RF problem for mul-trees (MulRF) as follows: Given a collection of multi-copy gene trees, find a singly-labeled species tree that minimizes the total RF distance from the input mul-trees. We develop and implement a fast SPR-based heuristic algorithm for the NP-hard MulRF problem.We compare the performance of the MulRF method (available at http://genome.cs.iastate.edu/CBL/MulRF/) with several gene tree parsimony approaches using gene tree simulations that incorporate gene tree error, gene duplications and losses, and/or lateral transfer. The MulRF method produces more accurate species trees than gene tree parsimony approaches. We also demonstrate that the MulRF method infers in minutes a credible plant species tree from a collection of nearly 2,000 gene trees. CONCLUSIONS: Our new phylogenetic inference method, based on a generalized RF distance, makes it possible to quickly estimate species trees from large genomic data sets. Since the MulRF method, unlike gene tree parsimony, is based on a generic tree distance measure, it is appealing for analyses of genomic data sets, in which many processes such as deep coalescence, recombination, gene duplication and losses as well as phylogenetic error may contribute to gene tree discord. In experiments, the MulRF method estimated species trees accurately and quickly, demonstrating MulRF as an efficient alternative approach for phylogenetic inference from large-scale genomic data sets.

Project description:BackgroundThe Iberian Peninsula is a diverse region that contains several different bioclimatic areas within one confined space, leading to high biodiversity. Portugal distinguishes itself in this regard by having a high count of spider species (829) and a remarkable number of endemic spider species (42) for its size (approximately 88,890 km2). However, only one non-endemic species (Macrothele calpeiana) is currently protected by the Natura 2000 network and no endemic spider species (aside from Anapistula ataecina) has been assessed according to the IUCN Red List criteria. The objective of this paper is to assess all non-assessed endemic species (41) as well as M. calpeiana.New informationThe 43 assessed species belong to 15 families, the richest being Zodariidae, Dysderidae, Linyphiidae and Gnaphosidae. In general and despite the lack of information on more than half the species, general patterns and trends could be found.Only 18 species (including M. calpeiana and A. ataecina) had enough data to allow their EOO (extent of occurrence) and AOO (area of occurrence) to be quantified. Of these, we modelled the distribution of 14 epigean species, eight of which were found to be widespread. The remaining six fulfilled at least one of the criteria for threatened species. Four species are troglobiont, all of which meet the EOO and AOO thresholds for threatened species. The remaining 25 Portuguese endemics had no reliable information on their range. Only nine species out of the 43 are estimated to be in decline and 11 are stable, with the majority of species having no information on trends (23 species).Forest areas, sand dunes, shrublands and caves host the majority of species. As such, the threats to Portuguese endemics reflect the diversity of habitats they occupy. Urbanisation and climate change seem to be the most important threats to these species, although other factors are also important and represented across the data.A considerable proportion of the currently known Portuguese endemic species can be found in national protected areas, with higher prominence to the Serras de Aire e Candeeiros, Douro Internacional, Vale do Guadiana, Sudoeste Alentejano e Costa Vicentina and Arrábida Natural Parks. These correspond mostly to areas that have been particularly well sampled during the last two decades.

Dataset Information

Inferring species trees from gene trees in a radiation of California trapdoor spiders (Araneae, Antrodiaetidae, Aliatypus).

Background

Methodology/principal findings

Conclusions/significance

Publications

Inferring species trees from gene trees in a radiation of California trapdoor spiders (Araneae, Antrodiaetidae, Aliatypus).

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