scholarly journals A phylogeny of the genus Limia (Teleostei: Poeciliidae) suggests a single-lake radiation nested in a Caribbean-wide allopatric speciation scenario

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Montrai Spikes ◽  
Rodet Rodríguez-Silva ◽  
Kerri-Ann Bennett ◽  
Stefan Bräger ◽  
James Josaphat ◽  
...  
Keyword(s):  
Incomplete Lineage Sorting ◽  
Strong Support ◽  
Greater Antilles ◽  
Lineage Sorting ◽  
Total N ◽  
Complete Sequences ◽  
History Of ◽  
Adaptive Radiations ◽  
The Caribbean ◽  
Local Radiation

Abstract Objective The Caribbean is an important global biodiversity hotspot. Adaptive radiations there lead to many speciation events within a limited period and hence are particularly prominent biodiversity generators. A prime example are freshwater fish of the genus Limia, endemic to the Greater Antilles. Within Hispaniola, nine species have been described from a single isolated site, Lake Miragoâne, pointing towards extraordinary sympatric speciation. This study examines the evolutionary history of the Limia species in Lake Miragoâne, relative to their congeners throughout the Caribbean. Results For 12 Limia species, we obtained almost complete sequences of the mitochondrial cytochrome b gene, a well-established marker for lower-level taxonomic relationships. We included sequences of six further Limia species from GenBank (total N  = 18 species). Our phylogenies are in concordance with other published phylogenies of Limia. There is strong support that the species found in Lake Miragoâne in Haiti are monophyletic, confirming a recent local radiation. Within Lake Miragoâne, speciation is likely extremely recent, leading to incomplete lineage sorting in the mtDNA. Future studies using multiple unlinked genetic markers are needed to disentangle the relationships within the Lake Miragoâne clade.

scholarly journals A phylogeny of the genus Limia (Teleostei: Poeciliidae) suggests a single-lake radiation nested in a Caribbean-wide allopatric speciation scenario

2020 ◽  
Author(s):  
Montrai Spikes ◽  
Rodet Rodríguez-Silva ◽  
Kerri-Ann Bennett ◽  
Stefan Bräger ◽  
James Josaphat ◽  
...  
Keyword(s):  
Incomplete Lineage Sorting ◽  
Strong Support ◽  
Greater Antilles ◽  
Lineage Sorting ◽  
Complete Sequences ◽  
History Of ◽  
Adaptive Radiations ◽  
The Caribbean ◽  
High Level

Abstract The Caribbean is one of the most important biodiversity hotspots on the planet due to the high level of species diversity and endemism in plants and animals. As elsewhere, adaptive radiations in the Caribbean lead to many speciation events within a limited period and hence are particularly prominent biodiversity generators. The general prediction from Island Biogeography that relates species richness to island size is valid for livebearing fishes in general in the Greater Antilles, where larger islands have higher numbers of species mainly due to in situ speciation. A prime example of this speciation process can be seen in the genus Limia, endemic to the Greater Antilles. Within Hispaniola, nine species have been described from a single isolated site, Lake Miragoâne, pointing towards extraordinary sympatric speciation in Limia. Few studies have examined the evolutionary history of the fishes found in Lake Miragoâne. Here, we address the gaps in present knowledge by providing a preliminary phylogeny of Limia and testing whether the species found in Lake Miragoâne may originated from an in situ radiation. We targeted the mitochondrial cytochrome b gene, a well-established marker for lower-level taxonomic relationships for which we obtained almost complete sequences for 13 species. The general topology of the phylogenies we produced are in concordance with other published phylogenies of Limia. There is also strong support that the species found in Lake Miragoâne in Haiti are indeed monophyletic (BS=97; PP=1.0), confirming the hypothesis of a recent local radiation. Within Lake Miragoâne, speciation is likely extremely recent, leading to incomplete lineage sorting in the mtDNA. Future studies are needed using multiple unlinked genetic markers to disentangle the relationships within the Lake Miragoâne clade.

scholarly journals A test statistic to quantify treelikeness in phylogenetics

2021 ◽  
Author(s):  
Caitlin Cherryh ◽  
Bui Quang Minh ◽  
Rob Lanfear
Keyword(s):  
Evolutionary History ◽  
Incomplete Lineage Sorting ◽  
Phylogenetic Analyses ◽  
Phylogenetic Network ◽  
Parametric Bootstrap ◽  
Lineage Sorting ◽  
Test Statistic ◽  
Sequence Alignments ◽  
Wide Range ◽  
History Of

AbstractMost phylogenetic analyses assume that the evolutionary history of an alignment (either that of a single locus, or of multiple concatenated loci) can be described by a single bifurcating tree, the so-called the treelikeness assumption. Treelikeness can be violated by biological events such as recombination, introgression, or incomplete lineage sorting, and by systematic errors in phylogenetic analyses. The incorrect assumption of treelikeness may then mislead phylogenetic inferences. To quantify and test for treelikeness in alignments, we develop a test statistic which we call the tree proportion. This statistic quantifies the proportion of the edge weights in a phylogenetic network that are represented in a bifurcating phylogenetic tree of the same alignment. We extend this statistic to a statistical test of treelikeness using a parametric bootstrap. We use extensive simulations to compare tree proportion to a range of related approaches. We show that tree proportion successfully identifies non-treelikeness in a wide range of simulation scenarios, and discuss its strengths and weaknesses compared to other approaches. The power of the tree-proportion test to reject non-treelike alignments can be lower than some other approaches, but these approaches tend to be limited in their scope and/or the ease with which they can be interpreted. Our recommendation is to test treelikeness of sequence alignments with both tree proportion and mosaic methods such as 3Seq. The scripts necessary to replicate this study are available at https://github.com/caitlinch/treelikeness

Phylogenetic relationships based on nuclear and plastid DNA sequences reveal recent diversification and discordant patterns of morphological evolution of the Chilean genera of Gilliesieae (Amaryllidaceae: Allioideae)

2020 ◽  
Vol 194 (1) ◽  
pp. 84-99
Author(s):  
Inelia Escobar ◽  
Eduardo Ruiz-Ponce ◽  
Paula J Rudall ◽  
Michael F Fay ◽  
Oscar Toro-Núñez ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Phylogenetic Relationships ◽  
Incomplete Lineage Sorting ◽  
Morphological Evolution ◽  
Strong Support ◽  
Plastid Dna ◽  
Lineage Sorting ◽  
Generic Level ◽  
Molecular Analyses ◽  
Floral Diversity

Abstract Gilliesieae are a South American tribe of Amaryllidaceae characterized by high floral diversity. Given different taxonomic interpretations and proposals for generic and specific relationships, a representative phylogenetic analysis is required to clarify the systematics of this group. The present study provides a framework for understanding phylogenetic relationships and contributing to the development of an appropriate taxonomic treatment of Gilliesieae. Molecular analyses, based on nuclear (ITS) and plastid DNA sequences (trnL-F and rbcL), resolve with strong support the monophyly of the tribe and the differentiation of two major clades. Clade I comprises the genera Gilliesia, Gethyum and Solaria and Clade II includes Miersia and Speea. These well-supported clades are mostly congruent with vegetative and karyotype characters rather than, e.g., floral symmetry. At the generic level, all molecular analyses reveal the paraphyly of Gilliesia and Miersia. Gethyum was found to be paraphyletic, resulting in the confirmation of Ancrumia as a distinct genus. Several instances of incongruent phylogenetic signals were found among data sets. The calibrated tree suggests a recent diversification of the tribe (Pliocene–Pleistocene), a contemporary process of speciation in which instances of hybridization and incomplete lineage sorting could explain patterns of paraphyly and incongruence of floral morphology.

Cuban Archaeology in the Caribbean

2016 ◽  
Keyword(s):  
Isotope Analysis ◽  
Greater Antilles ◽  
Environmental Archaeology ◽  
Indigenous Groups ◽  
History Of ◽  
Research Questions ◽  
The Caribbean ◽  
Research Initiatives ◽  
Patterns Of Interaction ◽  
Key Questions

Cuba is not only the largest island of the Caribbean but also the most centrally located one, as it is accessible from the mainland by different routes and was therefore subject to several waves of migration. The history of the early colonization of this island—and of the Greater Antilles in general—is extremely complex. The research initiatives presented in this book strive to solve some of the main problems in understanding that complexity, and to give answers to key questions regarding the patterns of successive migrations and colonization of the island, the patterns of interaction between the foraging and the agriculturalist groups, and the fate of the indigenous groups at the time of contact with the Spanish. A methodical multidisciplinary approach, necessary to tackle the full scope of the proposed research questions, is reflected in the variety of the contributions included in this volume, such as archaeology, physical anthropology, environmental archaeology, paleoecology; paleodemography; isotope analysis; bathymetry; paleobotany; linguistics; and ethnohistory. While the immediate focus of the book is region-specific, it will also contribute to ongoing debates in anthropological archaeology concerning migration and colonization; the importance of landscape and seascape in shaping human experience; the role that contact and interaction between different groups play in building identity; and the contribution of native groups to the biological and cultural identity of post-contact and modern societies.

scholarly journals C4 photosynthetic evolution : sub-types, diversity, and function within the grass tribe Paniceae

2017 ◽  
Author(s):  
◽  
Jacob Daniel Washburn
Keyword(s):  
Incomplete Lineage Sorting ◽  
Strong Support ◽  
Cell Types ◽  
Bioenergy Crops ◽  
Comparative Genomic ◽  
Lineage Sorting ◽  
Dna And Rna ◽  
Genomic Studies ◽  
Rna Expression Profiling ◽  
And Function

Most plants convert sunlight into chemical energy using a process known as C[subscript 3] photosynthesis. However, some of the world's most successful plants instead use the C[subscript 4] photosynthetic pathway which allows them to more efficiently use water, nitrogen, and solar energy. In the past 30 million years, C4 photosynthesis has convergently evolved from C3 over 60 times and new lineages are in the process of evolving even today. Because of this complex evolutionary history, C[subscript 4] is not "one" uniform photosynthetic type, but a diverse collection of photosynthetic sub-types that are classically grouped according to their use of three different biochemical pathways. The grass tribe Paniceae is especially interesting in this aspect because it contains all three of these biochemical subtypes as well as important food and bioenergy crops. To better understand the evolution of C[subscript 4] photosynthesis, DNA and RNA sequencing were undertaken for various species from within the Paniceae and used for phylogenetic and comparative genomic studies. Cell type specific RNA expression profiling for the two major C4 cell types was also completed for representative species of each C[subscript 4] sub-type. Streamlined bioinformatics pipelines for both chloroplast and nuclear phylogenetics were developed for processing the data. These analyses resulted in: 1) The first "genome scale" phylogenetic tree of the grass tribe Paniceae, 2) The clearest evidence to date of the evolutionary relationships between the three classically defined C[subscript 4] sub-types, 3) The most convincing results to date that the chloroplast and nuclear phylogenies of the Paniceae are incongruent, 4) Evidence that this chloroplast nuclear incongruence is likely due to introgression and/or incomplete lineage sorting, and 5) Strong support for sub-type mixing as well as the existence of a PCK sub-type.

scholarly journals Interrogating Genomic Data in the Phylogenetic Placement of Treeshrews Reveals Potential Sources of Conflict

2021 ◽  
Author(s):  
Alexander Knyshov ◽  
Yana Hrytsenko ◽  
Robert Literman ◽  
Rachel S Schwartz
Keyword(s):  
Incomplete Lineage Sorting ◽  
Phylogenetic Signal ◽  
Strong Support ◽  
Genomic Data ◽  
Phylogenetic Position ◽  
Lineage Sorting ◽  
Mammal Species ◽  
Small Magnitude ◽  
Locus Selection ◽  
Alternative Hypotheses

The position of some taxa on the Tree of Life remains controversial despite the increase in genomic data used to infer phylogenies. While analyzing large datasets alleviates stochastic errors, it does not prevent systematic errors in inference, caused by both biological (e.g., incomplete lineage sorting, hybridization) and methodological (e.g., incorrect modeling, erroneous orthology assessments) factors. In our study, we systematically investigated factors that could result in these controversies, using the treeshrew (Scandentia, Mammalia) as a study case. Recent studies have narrowed the phylogenetic position of treeshrews to three competing hypotheses: sister to primates and flying lemurs (Primatomorpha), sister to rodents and lagomorphs (Glires), or sister to a clade comprising all of these. We sampled 50 mammal species including three treeshrews, a selection of taxa from the potential sister groups, and outgroups. Using a large diverse set of loci, we assessed support for the alternative phylogenetic position of treeshrews. A plurality of loci support treeshrews as sister to rodents and lagomorphs; however, only a few loci exhibit strong support for any hypothesis. Surprisingly, we found that a subset of loci that strongly support the monophyly of Primates, support treeshrews as sister to primates and flying lemurs. The overall small magnitude of differences in phylogenetic signal among the alternative hypotheses suggests that these three groups diversified nearly simultaneously. However, with our large dataset and approach to examining support, we provide evidence for the hypothesis of treeshrews as sister to rodents and lagomorphs, while demonstrating why support for alternate hypotheses has been seen in prior work. We also suggest that locus selection can unwittingly bias results.

Molecular systematics and phylogeography of a widespread Neotropical avian lineage: evidence for cryptic speciation with protracted gene flow throughout the Late Quaternary

2020 ◽  
Author(s):  
Leonardo S Miranda ◽  
Bernardo O Prestes ◽  
Alexandre Aleixo
Keyword(s):  
Gene Flow ◽  
Incomplete Lineage Sorting ◽  
Late Quaternary ◽  
Integrative Approach ◽  
Lineage Sorting ◽  
Distribution Models ◽  
The North ◽  
History Of ◽  
Andean South America ◽  
Spatio Temporal

Abstract Here we use an integrative approach, including coalescent-based methods, isolation–migration and species distribution models, to infer population structure, divergence times and diversification in the two species of the genus Cymbilaimus (Aves, Thamnophilidae). Our results support a recent and rapid diversification with both incomplete lineage sorting and gene flow shaping the evolutionary history of Cymbilaimus. The spatio-temporal pattern of cladogenesis suggests that Cymbilaimus originated in the north/western portion of cis-Andean South America and then diversified into the Brazilian Shield and Central America after consolidation of the modern Amazonian drainage and the Andean range. This evolutionary scenario is explained by cycles of range expansion and dispersal, followed by isolation, and recurrent gene flow, during the last 1.2 Myr. Our results agree with those recently reported for other closely related suboscine lineages, whereby the window of introgression between closely related taxa remains open for up to a few million years after their original split. In Cymbilaimus, introgression was recurrent between C. lineatus and C. sanctaemariae, even after they acquired vocal and ecological differentiation, supporting the claim that at least in Neotropical suboscines, full reproductive compatibility may take millions of years to evolve and cannot be interpreted as synonymous with a lack of speciation.

literature review of the Polychaeta of the Caribbean Sea

Zootaxa ◽  
2012 ◽  
Vol 3596 (1) ◽  
pp. 1 ◽  
Author(s):  
HARLAN K. DEAN
Keyword(s):  
Caribbean Sea ◽  
Greater Antilles ◽  
South American ◽  
Polychaete Species ◽  
The North ◽  
Primary Literature ◽  
South American Region ◽  
History Of ◽  
The Caribbean

A list of all known polychaete species reported in the primary literature is presented for the Caribbean Sea. The most spe-cies-rich polychaete faunas are those of Cuba in the North Caribbean ecoregion and Trinidad-Tobago and Colombia in theSouth Caribbean ecoregion while the ecoregion with the greatest number of species is the Greater Antilles. While part ofthe explanation for these higher diversity areas may be due to collection effort, these areas may also be higher in speciesnumber as a result of being ecotones between the Gulf of Mexico in the north and the northern South American region tothe south. The most species-rich families are the Syllidae, Eunicidae, Nereididae, Polynoidae, Sabellidae, Serpulidae, Ter-ebellidae, and Spionidae. A brief discussion of the history of polychaete research identified many of the more importantworkers in the characterization of the polychaete fauna of the region. An analysis of the species-record accumulation curvefor polychaetes indicated that this fauna has not yet been fully characterized. One portion of the polychaete fauna identified as being especially poorly known is that from the deep-water areas of the Caribbean.

Ideology, Chiefly Power, and Material Culture: An Example from the Greater Antilles

1996 ◽  
Vol 7 (2) ◽  
pp. 114-131 ◽  
Author(s):  
L. Antonio Curet
Keyword(s):  
Material Culture ◽  
Puerto Rican ◽  
Cultural History ◽  
Cultural Change ◽  
Social Structures ◽  
Greater Antilles ◽  
Cultural Groups ◽  
The Social ◽  
History Of ◽  
The Caribbean

AbstractTemporal changes in material culture normally have been used by archaeologists to reconstruct the cultural history of an area or site. In the case of the Caribbean, shifts in artifactual style have been used to trace prehistoric migrations and interactions between different cultural groups. Unfortunately, there have been few attempts to explain these changes in terms of the social structures of these cultures. This paper reviews the archaeological evidence for cultural change in eastern Puerto Rico and proposes a model to explain it. Basically, the model suggests that changes in material culture in Puerto Rican prehistory are related to the development of social complexity. Shifts in decoration and types of artifacts are seen as an attempt by elite groups to have greater control over the symbolism represented in the artifacts in order to acquire and maintain their power. These changes are not abrupt, but gradual, as social organization evolves from simple to more complex chiefdoms.

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