Impact of the Partitioning Scheme on Divergence Times Inferred from Mammalian Genomic Data Sets

Data partitioning has long been regarded as an important parameter for phylogenetic inference. The division of heterogeneous multigene data sets into partitions with similar substitution patterns is known to increase the performance of probabilistic phylogenetic methods. However, the effect of the partitioning scheme on divergence time estimates has generally been ignored. To investigate the impact of data partitioning on the estimation of divergence times, we have constructed two genomic data sets. The first one with 15 nuclear genes comprising 50,928 bp were selected from the OrthoMam database; the second set was composed of complete mitochondrial genomes. We studied two partitioning schemes: concatenated supermatrices and partitioned gene analysis. We have also measured the impact of taxonomic sampling on the estimates. After drawing divergence time inferences using the uncorrelated relaxed clock in BEAST, we have compared the age estimates between the partitioning schemes. Our results show that, in general, both schemes resulted in similar chronological estimates, however the concatenated data sets were more efficient than the partitioned ones in attaining suitable effective sample sizes

FIGURE 3 in Molecular phylogeny and divergence time estimates of Penaeid Shrimp Lineages (Decapoda: Penaeidae)

FIGURE 3. The four major zoogeographical regions with the respective total number of species and endemic species found. Hatched regions represent the distributional area of penaeid shrimps (adapted from Dall et al. 1990).Published as part of <i>Voloch, Carolina M, Freire, Pablo R & Russo, Claudia A M, 2009, Molecular phylogeny and divergence time estimates of Penaeid Shrimp Lineages (Decapoda: Penaeidae), pp. 41-52 in Zootaxa 2107 (1)</i> on page 48, DOI: 10.11646/zootaxa.2107.1.2, <a href="http://zenodo.org/record/10093294">http://zenodo.org/record/10093294</a&gt

FIGURE 2. Penaeini ultrametric tree. Below a in Molecular phylogeny and divergence time estimates of Penaeid Shrimp Lineages (Decapoda: Penaeidae)

FIGURE 2. Penaeini ultrametric tree. Below a geological time-scale is shown.Published as part of <i>Voloch, Carolina M, Freire, Pablo R & Russo, Claudia A M, 2009, Molecular phylogeny and divergence time estimates of Penaeid Shrimp Lineages (Decapoda: Penaeidae), pp. 41-52 in Zootaxa 2107 (1)</i> on page 47, DOI: 10.11646/zootaxa.2107.1.2, <a href="http://zenodo.org/record/10093294">http://zenodo.org/record/10093294</a&gt

Assessing Genetic Diversity after Mangrove Restoration in Brazil: Why Is It So Important?

Vital for many marine and terrestrial species, and several other environmental services, such as carbon sink areas, the mangrove ecosystem is highly threatened due to the proximity of large urban centers and climate change. The forced fragmentation of this ecosystem affects the genetic diversity distribution among natural populations. Moreover, while restoration efforts have increased, few studies have analyzed how recently-planted areas impact the original mangrove genetic diversity. We analyzed the genetic diversity of two mangroves species (Laguncularia racemosa and Avicennia schaueriana) in three areas in Brazil, using inter-simple sequence repeat (ISSR) markers. Using the local approach, we identified the genetic diversity pool of a restored area compared to nearby areas, including the remnant plants inside the restored area, one well-conserved population at the shore of Guanabara Bay, and one impacted population in Araçá Bay. The results for L. racemosa showed that the introduced population has lost genetic diversity by drift, but remnant plants with high genetic diversity or incoming propagules could help improve overall genetic diversity. Avicennia schaueriana showed similar genetic diversity, indicating an efficient gene flow. The principal component analysis showing different connections between both species indicate differences in gene flow and dispersal efficiencies, highlighting the needed for further studies. Our results emphasize that genetic diversity knowledge and monitoring associated with restoration actions can help avoid bottlenecks and other pitfalls, especially for the mangrove ecosystem

Data from: Diversification of the genus Anopheles and a Neotropical clade from the Late Cretaceous

The Anopheles genus is a member of the Culicidae family and consists of approximately 460 recognized species. The genus is composed of 7 subgenera with diverse geographical distributions. Despite its huge medical importance, a consensus has not been reached on the phylogenetic relationships among Anopheles subgenera. We assembled a comprehensive dataset comprising the COI, COII and 5.8S rRNA genes and used maximum likelihood and Bayesian inference to estimate the phylogeny and divergence times of six out of the seven Anopheles subgenera. Our analysis reveals a monophyletic group composed of the three exclusively Neotropical subgenera, Stethomyia, Kerteszia and Nyssorhynchus, which began to diversify in the Late Cretaceous, at approximately 90 Ma. The inferred age of the last common ancestor of the Anopheles genus was ca. 110 Ma. The monophyly of all Anopheles subgenera was supported, although we failed to recover a significant level of statistical support for the monophyly of the Anopheles genus. The ages of the last common ancestors of the Neotropical clade and the Anopheles and Cellia subgenera were inferred to be at the Late Cretaceous (ca. 90 Ma). Our analysis failed to statistically support the monophyly of the Anopheles genus because of an unresolved polytomy between Bironella and A. squamifemur

Diversification of the Genus Anopheles and a Neotropical Clade from the Late Cretaceous.

The Anopheles genus is a member of the Culicidae family and consists of approximately 460 recognized species. The genus is composed of 7 subgenera with diverse geographical distributions. Despite its huge medical importance, a consensus has not been reached on the phylogenetic relationships among Anopheles subgenera. We assembled a comprehensive dataset comprising the COI, COII and 5.8S rRNA genes and used maximum likelihood and Bayesian inference to estimate the phylogeny and divergence times of six out of the seven Anopheles subgenera. Our analysis reveals a monophyletic group composed of the three exclusively Neotropical subgenera, Stethomyia, Kerteszia and Nyssorhynchus, which began to diversify in the Late Cretaceous, at approximately 90 Ma. The inferred age of the last common ancestor of the Anopheles genus was ca. 110 Ma. The monophyly of all Anopheles subgenera was supported, although we failed to recover a significant level of statistical support for the monophyly of the Anopheles genus. The ages of the last common ancestors of the Neotropical clade and the Anopheles and Cellia subgenera were inferred to be at the Late Cretaceous (ca. 90 Ma). Our analysis failed to statistically support the monophyly of the Anopheles genus because of an unresolved polytomy between Bironella and A. squamifemur

Ancestral area reconstruction conducted using the maximum likelihood method in the APE package.

<p>Circles depict the relative probabilities of each region. Color codes are as follows: green—Africa; yellow—Americas; blue—Southeast Asia and the Pacific; gray—Europe plus Middle East; and red—India plus West Asia.</p

Phylogeny of the <i>Anopheles</i> genus.

<p>(a) Maximum likelihood tree with aLRT statistical support. (b) Bayesian inference tree with clade posterior probabilities.</p

GenBank accession numbers of sequences.

<p>GenBank accession numbers of sequences.</p