Drivers of Cape Verde archipelagic endemism in keyhole limpets

Oceanic archipelagos are the ideal setting for investigating processes that shape species assemblages. Focusing on keyhole limpets, genera Fissurella and Diodora from Cape Verde Islands, we used an integrative approach combining molecular phylogenetics with ocean transport simulations to infer species distribution patterns and analyse connectivity. Dispersal simulations, using pelagic larval duration and ocean currents as proxies, showed a reduced level of connectivity despite short distances between some of the islands. It is suggested that dispersal and persistence driven by patterns of oceanic circulation favouring self-recruitment played a primary role in explaining contemporary species distributions. Mitochondrial and nuclear data revealed the existence of eight Cape Verde endemic lineages, seven within Fissurella, distributed across the archipelago, and one within Diodora restricted to Boavista. The estimated origins for endemic Fissurella and Diodora were 10.2 and 6.7 MY, respectively. Between 9.5 and 4.5 MY, an intense period of volcanism in Boavista might have affected Diodora, preventing its diversification. Having originated earlier, Fissurella might have had more opportunities to disperse to other islands and speciate before those events. Bayesian analyses showed increased diversification rates in Fissurella possibly promoted by low sea levels during Plio-Pleistocene, which further explain differences in species richness between both genera.FCT - Portuguese Science Foundation [SFRH/BPD/109685/2015, SFRH/BPD/111003/2015]; Norte Portugal Regional Operational Program (NORTE), under the PORTUGAL Partnership Agreement, through the European Regional Development Fund (ERDF) [MARINFO - NORTE-01-0145-FEDER-000031]info:eu-repo/semantics/publishedVersio

Different diversity-dependent declines in speciation rate unbalances species richness in terrestrial slugs

Two genera of terrestrial slugs (Arion and Geomalacus) display a striking disproportion in species richness in the Iberian Peninsula. While there are 17 Iberian endemic species in Arion, morphological criteria only recognize four species within Geomalacus. Sequence data were used to test whether these differences could result from: (1) cryptic diversity within Geomalacus; (2) an earlier origin for Arion (older clades are expected to accumulate more species); (3) distinct patterns of diversification rates (higher initial speciation rates in Arion), and (4) some combination of the above factors (e.g., an older clade with higher speciation rates). Species delimitation tests based on mitochondrial and nuclear data revealed eight cryptic lineages within Geomalacus that lessened the asymmetry; nevertheless, the disparity required further investigation. No meaningful differences in crown group ages of each recovered clade were found. Regardless the different premises of the two equally plausible diversification models (similar initial speciation rates vs. higher initial speciation rates in Geomalacus), both coincide on diversity-dependent diversification for the two groups but weaker rate declines in Arion best explains the observed asymmetry in species richness. Also, the broader environmental tolerance combined with a faster dispersal and wider distribution may have represented an evolutionary advantage for Arion.FCT (Fundacao para a Ciencia e Tecnologia, Portugal) [SFRH/BPD/109685/2015]; FSE (Fundo Social Europeu). [SFRH/BD/30024/2006]; FCT strategic plan [UID/Multi/04326/2013]info:eu-repo/semantics/publishedVersio

Genetic Networking of the Bemisia tabaci Cryptic Species Complex Reveals Pattern of Biological Invasions

BACKGROUND: A challenge within the context of cryptic species is the delimitation of individual species within the complex. Statistical parsimony network analytics offers the opportunity to explore limits in situations where there are insufficient species-specific morphological characters to separate taxa. The results also enable us to explore the spread in taxa that have invaded globally. METHODOLOGY/PRINCIPAL FINDINGS: Using a 657 bp portion of mitochondrial cytochrome oxidase 1 from 352 unique haplotypes belonging to the Bemisia tabaci cryptic species complex, the analysis revealed 28 networks plus 7 unconnected individual haplotypes. Of the networks, 24 corresponded to the putative species identified using the rule set devised by Dinsdale et al. (2010). Only two species proposed in Dinsdale et al. (2010) departed substantially from the structure suggested by the analysis. The analysis of the two invasive members of the complex, Mediterranean (MED) and Middle East - Asia Minor 1 (MEAM1), showed that in both cases only a small number of haplotypes represent the majority that have spread beyond the home range; one MEAM1 and three MED haplotypes account for >80% of the GenBank records. Israel is a possible source of the globally invasive MEAM1 whereas MED has two possible sources. The first is the eastern Mediterranean which has invaded only the USA, primarily Florida and to a lesser extent California. The second are western Mediterranean haplotypes that have spread to the USA, Asia and South America. The structure for MED supports two home range distributions, a Sub-Saharan range and a Mediterranean range. The MEAM1 network supports the Middle East - Asia Minor region. CONCLUSION/SIGNIFICANCE: The network analyses show a high level of congruence with the species identified in a previous phylogenetic analysis. The analysis of the two globally invasive members of the complex support the view that global invasion often involve very small portions of the available genetic diversity

Species Tree Estimation for the Late Blight Pathogen, Phytophthora infestans, and Close Relatives

To better understand the evolutionary history of a group of organisms, an accurate estimate of the species phylogeny must be known. Traditionally, gene trees have served as a proxy for the species tree, although it was acknowledged early on that these trees represented different evolutionary processes. Discordances among gene trees and between the gene trees and the species tree are also expected in closely related species that have rapidly diverged, due to processes such as the incomplete sorting of ancestral polymorphisms. Recently, methods have been developed for the explicit estimation of species trees, using information from multilocus gene trees while accommodating heterogeneity among them. Here we have used three distinct approaches to estimate the species tree for five Phytophthora pathogens, including P. infestans, the causal agent of late blight disease in potato and tomato. Our concatenation-based “supergene” approach was unable to resolve relationships even with data from both the nuclear and mitochondrial genomes, and from multiple isolates per species. Our multispecies coalescent approach using both Bayesian and maximum likelihood methods was able to estimate a moderately supported species tree showing a close relationship among P. infestans, P. andina, and P. ipomoeae. The topology of the species tree was also identical to the dominant phylogenetic history estimated in our third approach, Bayesian concordance analysis. Our results support previous suggestions that P. andina is a hybrid species, with P. infestans representing one parental lineage. The other parental lineage is not known, but represents an independent evolutionary lineage more closely related to P. ipomoeae. While all five species likely originated in the New World, further study is needed to determine when and under what conditions this hybridization event may have occurred

Land bridge calibration of rates of molecular evolution in a widespread rodent

There is mounting evidence that rates of molecular evolution decay over recent timescales. Care is needed, therefore, to apply appropriate rates whenever molecular variation is analysed within a temporal context. Given their focus on recent events, intraspecific phylogeographic and demographic studies are particularly vulnerable to erroneous application of rates appropriate to longer periods of evolution and divergence. Rates for recent molecular evolution can be inferred directly from the DNA sequences themselves, but external geophysical events may also be used for calibration. In particular, the formation and loss of land bridges can provide an opportunity to calibrate intraspecific genealogies, estimate molecular rates and infer the absolute timing or scale of demographic changes. The Eurasian field vole Microtus agrestis is an exceptional system with which to examine recent demographic change and divergence in a wild mammal, because of its clear-cut pattern of molecular variation, being composed of three evolutionarily significant units (ESUs) that are reciprocally monophyletic for mitochondrial, sex-chromosome and autosomal markers. These three lineages are confined to northern Eurasia, southern Europe and western Iberia. The northern ESU is in turn comprised of six parapatric mitochondrial lineages, one of them confined to northern Britain. The restricted distribution of this lineage can be associated with the Holocene land bridge connecting Britain with mainland Europe, which permits the temporal calibration of the genealogy and the association of demographic changes with specific climatic episodes. The resulting estimate of the mitochondrial protein-coding substitution rate is very high (ca. 4 × 10−7 substitutions/site/year), similar to mutation rates measured from pedigrees, i.e. contemporary evolution. The reliability of this estimate is considered

Towards resolving the double classification in Erythraeus (Actinotrichida: Erythraeidae): matching larvae with adults using 28S sequence data and experimental rearing

The taxonomy of free-living adults and heteromorphic parasitic larvae of Parasitengona mites has in the past been treated independently resulting in a double classification. Correct linkage of names still remains unknown for many species. A holistic understanding of species is imperative for understanding their role in ecosystems. This is particularly true for groups like parasitengone mites with a radically altered lifestyle during development—parasitic to predatory. Here, we infer linkages of three nominal species of Erythraeus, using matching with 28S DNA sequence data from field-collected specimens and through laboratory rearing. The general mixed Yule coalescent method (GMYC) was used to explicitly test if field-collected specimens representing heteromorphic life instars were conspecific. The field-collected larvae were allocated to adults of Erythraeus cinereus and Erythraeus regalis, respectively. Laboratory rearing of the same two species confirmed the matching done by DNA. Rearing was also successful for Erythraeus phalangoides after eggs were treated to an imitated winter diapause. This integrative taxonomic approach of molecular, morphological, and rearing data resulted in the following synonyms: E. phalangoides (De Geer, 1778) [= Erythraeus adrastus(Southcott, 1961), syn. nov.], E. cinereus (Dugès, 1834) [= Erythraeus jowitae Haitlinger, 1987, syn. nov.], and E. regalis (C.L. Koch, 1837) [= Erythraeus kuyperi (Oudemans, 1910), syn. nov., = Erythraeus gertrudae Haitlinger, 1987, syn. nov.]. The molecular evidence confirmed the separate identity of three further members of the genus. We provide redescriptions of E. phalangoides, E. cinereus, and E. regalis after modern standards, and neotypes are designated