Investigating evolutionary lag using the species-pairs evolutionary lag test (SPELT)

Evolution ◽  
2014 ◽  
Vol 69 (1) ◽  
pp. 245-253 ◽  
Author(s):  
Charles L. Nunn ◽  
Natalie Cooper
Keyword(s):  
Species Pairs ◽  
Evolutionary Lag

scholarly journals Species-Specific Segregation of Gender-Associated Mitochondrial DNA Types in an Area Where Two Mussel Species (Mytilus edulis and M. trossulus) Hybridize

Genetics ◽  
1996 ◽  
Vol 143 (3) ◽  
pp. 1359-1367 ◽  
Author(s):  
Carlos Saavedra ◽  
Donald T Stewart ◽  
Rebecca R Stanwood ◽  
Eleftherios Zouros
Keyword(s):  
Mytilus Edulis ◽  
The Other ◽  
Allozyme Analysis ◽  
Mussel Species ◽  
Species Origin ◽  
Species Pairs ◽  
Nuclear Background ◽  
Species Specific ◽  
Dna Types ◽  
Fertile Hybrids

Abstract In each of the mussel species Mytilus edulis and M. trossulus there exist two types of mtDNA, the F type transmitted through females and the M type transmitted through males. Because the two species produce fertile hybrids in nature, F and M types of one may introgress into the other. We present the results from a survey of a population in which extensive hybridization occurs between these two species. Among specimens classified as “pure” M. edulis or “pure” M. trossulus on the basis of allozyme analysis, we observed no animal that carried the F or the M mitotype of the other species. In most animals of mixed nuclear background, an individual's mtDNA came from the species that contributed the majority of the individual's nuclear genes. Most importantly, the two mtDNA types in post-F1 male hybrids were of the same species origin. We interpret this to mean that there are intrinsic barriers to the exchange of mtDNA between these two species. Because such barriers were not noted in other hybridizing species pairs (many being even less interfertile than M. edulis and M. trossulus), their presence in Mytilus could be another feature of the unusual mtDNA system in this genus.

scholarly journals Evaluating the role of contracting and expanding rainforest in initiating cycles of speciation across the Isthmus of Panama

2012 ◽  
Vol 279 (1742) ◽  
pp. 3520-3526 ◽  
Author(s):  
Brian Tilston Smith ◽  
Amei Amei ◽  
John Klicka
Keyword(s):  
Bird Species ◽  
Tropical Regions ◽  
Isthmus Of Panama ◽  
Species Pairs ◽  
The Matrix ◽  
High Species Richness ◽  
The Rich ◽  
The Tropics ◽  
The Impact

Climatic and geological changes across time are presumed to have shaped the rich biodiversity of tropical regions. However, the impact climatic drying and subsequent tropical rainforest contraction had on speciation has been controversial because of inconsistent palaeoecological and genetic data. Despite the strong interest in examining the role of climatic change on speciation in the Neotropics there has been few comparative studies, particularly, those that include non-rainforest taxa. We used bird species that inhabit humid or dry habitats that dispersed across the Panamanian Isthmus to characterize temporal and spatial patterns of speciation across this barrier. Here, we show that these two assemblages of birds exhibit temporally different speciation time patterns that supports multiple cycles of speciation. Evidence for these cycles is further corroborated by the finding that both assemblages consist of ‘young’ and ‘old’ species, despite dry habitat species pairs being geographically more distant than pairs of humid habitat species. The matrix of humid and dry habitats in the tropics not only allows for the maintenance of high species richness, but additionally this study suggests that these environments may have promoted speciation. We conclude that differentially expanding and contracting distributions of dry and humid habitats was probably an important contributor to speciation in the tropics.

Patterns of morphological diversity among and within arcid bivalve species pairs separated by the Isthmus of Panama

2001 ◽  
Vol 75 (3) ◽  
pp. 590-606 ◽  
Author(s):  
Peter B. Marko ◽  
Jeremy B. C. Jackson
Keyword(s):  
Morphological Variation ◽  
Fossil Record ◽  
Eastern Pacific ◽  
Nominal Species ◽  
Western Atlantic ◽  
Isthmus Of Panama ◽  
Species Pairs ◽  
Recent Species ◽  
Discriminant Analyses ◽  
Collection Sites

Geminate species are morphologically similar sister-species found on either side of the Isthmus of Panama. The existence of all geminates in the tropical Eastern Pacific ocean and the Caribbean Sea is most often explained by vicariance: closure of the Central American Seaway 3.1 to 3.5 Ma simultaneously isolated populations of species with amphi-American distributions. In this paper, we test the potential of morphological measurements for discriminating between Recent geminate species pairs from three genera (Arca, Arcopsis, and Barbatia) in the bivalve family Arcidae and examine the prospects for distinguishing nominal species in the fossil record. Fourteen morphological variables were used to characterize shell shape and multivariate methods were used to discriminate between five Recent species pairs. Collection sites were also used as a priori groups for discrimination to describe patterns of intraspecific morphological variation and to evaluate differences among samples from different geographic regions.On average, 84 percent of specimens within geminate pairs are classified correctly following five separate discriminant analyses with nominal species as the grouping variable. Although all but one arcid species pair are discriminated with high statistical significance, some collection sites within species are highly morphologically distinct. Overall, a large proportion of specimens from each collection locality (79 percent on average) can be classified correctly to site although no single site possessed a multivariate centroid that was significantly different from all other conspecific centroids. The distinctiveness of some collection sites, however, raises the possibility that some nominal species may harbor cryptic species, indicating the need for wider geographic surveys of both molecular and morphological variation within geminate species pairs.The eigenvalue coefficients derived from the Recent samples of one geminate pair (Arca mutabilis and A. imbricata) were used to assess the potential for identifying arcid species in the fossil record. Discriminant analyses of fossil Arca indicate that the forms that characterize Recent A. mutabilis and A. imbricata are present in the fossil record as far back as the Late Early Miocene, in the Cantaure Formation of Venezuela. Because a deep water connection between the Eastern Pacific and Western Atlantic existed until the Middle Miocene, the morphological differences associated with Recent A. mutabilis and A. imbricata likely existed well before the rising Isthmus affected ocean circulation patterns in tropical America. Therefore, despite great overall morphological similarity, these putative geminate species likely have a time of divergence that is at least four times older than final seaway closure. The geographic distribution of fossils also suggests that morphological forms associated with each Recent species had amphi-American distributions both before and after isthmus formation but are now geographically restricted to either side of the isthmus in the Recent fauna.

scholarly journals Multi-modal signal evolution in birds: re-examining a standard proxy for sexual selection

2018 ◽  
Vol 285 (1889) ◽  
pp. 20181557 ◽  
Author(s):  
Christopher R. Cooney ◽  
Hannah E. A. MacGregor ◽  
Nathalie Seddon ◽  
Joseph A. Tobias
Keyword(s):  
Sexual Selection ◽  
Interspecific Interactions ◽  
Habitat Type ◽  
Negative Relationship ◽  
Key Factors ◽  
Phenotypic Data ◽  
Species Pairs ◽  
Multiple Alternative ◽  
Mating Signal ◽  
Diversification Hypothesis

Sexual selection is proposed to be an important driver of speciation and phenotypic diversification in animal systems. However, previous phylogenetic tests have produced conflicting results, perhaps because they have focused on a single signalling modality (visual ornaments), whereas sexual selection may act on alternative signalling modalities (e.g. acoustic ornaments). Here, we compile phenotypic data from 259 avian sister species pairs to assess the relationship between visible plumage dichromatism—a standard index of sexual selection in birds—and macroevolutionary divergence in the other major avian signalling modality: song. We find evidence for a strong negative relationship between the degree of plumage dichromatism and divergence in song traits, which remains significant even when accounting for other key factors, including habitat type, ecological divergence and interspecific interactions. This negative relationship is opposite to the pattern expected by a straightforward interpretation of the sexual selection–diversification hypothesis, whereby higher levels of dichromatism indicating strong sexual selection should be related to greater levels of mating signal divergence regardless of signalling modality. Our findings imply a ‘trade-off’ between the elaboration of visual ornaments and the diversification of acoustic mating signals, and suggest that the effects of sexual selection on diversification can only be determined by considering multiple alternative signalling modalities.

scholarly journals Base-substitution mutation rate across the nuclear genome of Alpheus snapping shrimp and the timing of isolation by the Isthmus of Panama

2020 ◽  
Author(s):  
Katherine Silliman ◽  
Jane L. Indorf ◽  
Nancy Knowlton ◽  
William E. Browne ◽  
Carla Hurt
Keyword(s):  
Mutation Rate ◽  
Sequence Data ◽  
Nuclear Genome ◽  
Base Substitution ◽  
Snapping Shrimp ◽  
Isthmus Of Panama ◽  
Species Pairs ◽  
Genotype By Sequencing ◽  
Independent Calibration ◽  
Taxonomic Groups

AbstractThe formation of the Isthmus of Panama and final closure of the Central American Seaway (CAS) provides an independent calibration point for examining the rate of DNA substitutions. This vicariant event has been widely used to estimate the substitution rate across mitochondrial genomes and to date evolutionary events in other taxonomic groups. Nuclear sequence data is increasingly being used to complement mitochondrial datasets for phylogenetic and evolutionary investigations; these studies would benefit from information regarding the rate and pattern of DNA substitutions derived from the nuclear genome. To estimate this genomewide neutral mutation rate (μ), genotype-by-sequencing (GBS) datasets were generated for three transisthmian species pairs in Alpheus snapping shrimp. Using a Bayesian coalescent approach (G-PhoCS) applied to 44,960 GBS loci, we estimated μ to be 2.64E-9 substitutions/site/year, when calibrated with the closure of the CAS at 3 Ma. This estimate is remarkably similar to experimentally derived mutation rates in model arthropod systems, strengthening the argument for a recent closure of the CAS. To our knowledge this is the first use of transisthmian species pairs to calibrate the rate of molecular evolution from GBS data.

scholarly journals Rapid divergence in independent aspects of the compatibility phenotype in the Spiroplasma/Drosophila interaction

2021 ◽  
Author(s):  
Joanne S. Griffin ◽  
Michael Gerth ◽  
Gregory D. D. Hurst
Keyword(s):  
Vertical Transmission ◽  
Host Species ◽  
High Efficiency ◽  
Host Shift ◽  
Direct Selection ◽  
New Host ◽  
Host Shifts ◽  
Species Pairs ◽  
Novel Host ◽  
Rapid Divergence

AbstractHeritable symbionts represent important components of host biology, both as antagonistic reproductive parasites and as beneficial protective partners. An important component of heritable microbes’ biology is their ability to establish in new host species, a process equivalent to a host shift for an infectiously transmitted parasite or pathogen. For a host shift to occur, the symbiont must be compatible with the host: it must not cause excess pathology, must have good vertical transmission, and possess a drive phenotype that enables spread. Classically, compatibility has been considered a declining function of genetic distance between novel and ancestral host species. Here we investigate the evolutionary lability of compatibility to heritable microbes by comparing the capacity for a symbiont to establish in two novel host species equally related to the ancestral host. Compatibility of the protective Spiroplasma from D. hydei with D. simulans and D. melanogaster was tested. The Spiroplasma had contrasting compatibility in these two host species. The transinfection showed pathology and low vertical transmission in D. melanogaster but was asymptomatic and transmitted with high efficiency in D. simulans. These results were not affected by the presence/absence of Wolbachia in either of the two species. The pattern of protection was not congruent with that for pathology/transmission, with protection being weaker in the D. simulans, the host in which Spiroplasma was asymptomatic and transmitted well. Further work indicated pathological interactions occurred in D. sechellia and D. yakuba, indicating that D. simulans was unusual in being able to carry the symbiont without damage. The differing compatibility of the symbiont with these closely related host species emphasises first the rapidity with which host-symbiont compatibility evolves despite compatibility itself not being subject to direct selection, and second the independence of the different components of compatibility (pathology, transmission, protection). This requirement to fit three different independently evolving aspects of compatibility, if commonly observed, is likely to be a major feature limiting the rate of host shifts. Moving forward, the variation between sibling species pairs observed above provides an opportunity to identify the mechanisms behind variable compatibility between closely related host species, which will drive hypotheses as to the evolutionary drivers of compatibility variation.

scholarly journals Sympatry drives colour and song evolution in wood-warblers (Parulidae)

2021 ◽  
Vol 288 (1942) ◽  
pp. 20202804
Author(s):  
Richard K. Simpson ◽  
David R. Wilson ◽  
Allison F. Mistakidis ◽  
Daniel J. Mennill ◽  
Stéphanie M. Doucet
Keyword(s):  
Related Species ◽  
Species Recognition ◽  
Sympatric Species ◽  
Signal Evolution ◽  
Wood Warblers ◽  
Mixed Support ◽  
Species Pairs ◽  
Song Divergence ◽  
Signal Diversity ◽  
Signal Divergence

Closely related species often exhibit similarities in appearance and behaviour, yet when related species exist in sympatry, signals may diverge to enhance species recognition. Prior comparative studies provided mixed support for this hypothesis, but the relationship between sympatry and signal divergence is likely nonlinear. Constraints on signal diversity may limit signal divergence, especially when large numbers of species are sympatric. We tested the effect of sympatric overlap on plumage colour and song divergence in wood-warblers (Parulidae), a speciose group with diverse visual and vocal signals. We also tested how number of sympatric species influences signal divergence. Allopatric species pairs had overall greater plumage and song divergence compared to sympatric species pairs. However, among sympatric species pairs, plumage divergence positively related to the degree of sympatric overlap in males and females, while male song bandwidth and syllable rate divergence negatively related to sympatric overlap. In addition, as the number of species in sympatry increased, average signal divergence among sympatric species decreased, which is likely due to constraints on warbler perceptual space and signal diversity. Our findings reveal that sympatry influences signal evolution in warblers, though not always as predicted, and that number of sympatric species can limit sympatry's influence on signal evolution.

scholarly journals Genome assembly, structural variants, and genetic differentiation between Lake Whitefish young species pairs (Coregonus sp.) with long and short reads

2022 ◽  
Author(s):  
Claire M&eacuterot ◽  
Kristina S R Stenl&oslashkk ◽  
Clare Venney ◽  
Martin Laporte ◽  
Michel Moser ◽  
...  
Keyword(s):  
Transposable Elements ◽  
Genetic Architecture ◽  
Large Fraction ◽  
Sympatric Species ◽  
Secondary Contact ◽  
Species Differentiation ◽  
Lake Whitefish ◽  
Structural Variants ◽  
Species Pairs ◽  
Long Read

The parallel evolution of nascent pairs of ecologically differentiated species offers an opportunity to get a better glimpse at the genetic architecture of speciation. Of particular interest is our recent ability to consider a wider range of genomic variants, not only single-nucleotide polymorphisms (SNPs), thanks to long-read sequencing technology. We can now identify structural variants (SVs) like insertions, deletions, and other structural rearrangements, allowing further insights into the genetic architecture of speciation and how different variants are involved in species differentiation. Here, we investigated genomic patterns of differentiation between sympatric species pairs (Dwarf and Normal) belonging to the Lake Whitefish (Coregonus clupeaformis) species complex. We assembled the first reference genomes for both Dwarf and Normal Lake Whitefish, annotated the transposable elements, and analysed the genome in the light of related coregonid species. Next, we used a combination of long-read and short-read sequencing to characterize SVs and genotype them at population-scale using genome-graph approaches, showing that SVs cover five times more of the genome than SNPs. We then integrated both SNPs and SVs to investigate the genetic architecture of species differentiation in two different lakes and highlighted an excess of shared outliers of differentiation. In particular, a large fraction of SVs differentiating the two species was driven by transposable elements (TEs), suggesting that TE accumulation during a period of allopatry predating secondary contact may have been a key process in the speciation of the Dwarf and Normal Whitefish. Altogether, our results suggest that SVs play an important role in speciation and that by combining second and third generation sequencing we now have the ability to integrate SVs into speciation genomics.

scholarly journals Ongoing production of low-fitness hybrids limits range overlap between divergent cryptic species

2021 ◽  
Author(s):  
Else K. Mikkelsen ◽  
Darren Irwin
Keyword(s):  
First Generation ◽  
Sex Chromosome ◽  
Genomic Variation ◽  
F1 Hybrids ◽  
The Pacific ◽  
Species Pairs ◽  
Genetic Clusters ◽  
Range Overlap ◽  
Female Specific

AbstractContact zones between recently-diverged taxa provide opportunities to examine the causes of reproductive isolation and to examine the processes that determine whether two species can coexist over a broad region. The Pacific Wren (Troglodytes pacificus) and the Winter Wren (Troglodytes hiemalis) are two morphologically similar songbird species that started diverging about 4 million years ago, older than most sister species pairs. The ranges of these species come into narrow contact in western Canada, where the two species remain distinct in sympatry. To assess evidence for differentiation, hybridization, and introgression in this system, we examined variation in over 250,000 single nucleotide polymorphism markers distributed across the genomes of the two species. The two species formed highly divergent genetic clusters, consistent with long-term differentiation. In a set of 75 individuals from allopatry and sympatry, two first-generation hybrids (i.e., F1’s) were detected, indicating only moderate levels of assortative mating between these taxa. We found no recent backcrosses or F2’s or other evidence of recent breeding success of F1 hybrids, indicating very low or zero fitness of F1 hybrids. Examination of genomic variation shows evidence for only a single backcrossing event in the distant past. The sizeable rate of hybridization combined with very low fitness of F1 hybrids is expected to result in a population sink in the contact zone, largely explaining the narrow overlap of the two species. If such dynamics are common in nature, they could explain the narrow range overlap often observed between pairs of closely related species. Additionally, we present evidence for a rare duplication of a large chromosomal segment from an autosome to the W chromosome, the female-specific sex chromosome in birds.

scholarly journals Asosiasi vegetasi tanaman rambatan ketak (Lygodium circinatum (Burm.) Sw.) di KPHL Rinjani Barat, Pulau Lombok, Nusa Tenggara Barat

1996 ◽  
Vol 13 (2) ◽  
pp. 85-94
Author(s):  
Endah Wahyuningsih ◽  
◽  
Eny Faridah ◽  
Budiadi Budiadi ◽  
Atus Syahbudin ◽  
...  
Keyword(s):  
Host Plant ◽  
Host Plants ◽  
Strong Association ◽  
Systematic Sampling ◽  
Species Pairs ◽  
Survey Technique ◽  
Species Type

Ketak (Lygodium circinatum (Burm.) Sw. is a fern plant and its growth requires other plants as a host plant for climbing of tendrils to get light. Information of vegetation association of host plant is needed, due to it is considered to have an influence on growth and productivity. This data and information is important to develop a strategy of ketak for cultivation and conservation. This research was aimed to determine vegetation association of ketak host plant in its habitat. The study applied purposive systematic sampling by survey technique based on altitude i.e. 0-249, 250-499 and 500-750 m asl. There are 10 of observation plot with dimension of 20 m x 20 m. In each plot, an analysis of vegetation association of ketak host plant to determine association between species, type of interaction and index of association between species of ketak host plant. The results showed that vegetation association of ketak host plants in each altitude classification which had a positive and strong association were 14 pairs species in altitude of 0-249 m asl, and 8 pairs species in altitude 250 – 499 m asl, and also in altitude 500 – 750 m asl had 15 pairs species. Altitude 500 - 750 m asl, shows the association of vegetation with the highest combination of species pairs.

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