Gene flow in phylogenomics: Sequence capture resolves species limits and biogeography of Afromontane forest endemic frogs from the Cameroon Highlands

In the ancillariid genus Amalda, the shell is character rich and 96 described species are currently treated as valid. Based on shell morphology, several subspecies have been recognized within Amalda hilgendorfi, with a combined range extending at depths of 150–750 m from Japan to the South-West Pacific. A molecular analysis of 78 specimens from throughout this range shows both a weak geographical structuring and evidence of gene flow at the regional scale. We conclude that recognition of subspecies (richeri Kilburn & Bouchet, 1988, herlaari van Pel, 1989, and vezzaroi Cossignani, 2015) within A. hilgendorfi is not justified. By contrast, hilgendorfi-like specimens from the Mozambique Channel and New Caledonia are molecularly segregated, and so are here described as new, as Amalda miriky sp. nov. and A. cacao sp. nov., respectively. The New Caledonia Amalda montrouzieri complex is shown to include at least three molecularly separable species, including A. allaryi and A. alabaster sp. nov. Molecular data also confirm the validity of the New Caledonia endemics Amalda aureomarginata, A. fuscolingua, A. bellonarum, and A. coriolis. The existence of narrow range endemics suggests that the species limits of Amalda with broad distributions, extending, e.g., from Japan to Taiwan (A. hinomotoensis) or even Indonesia, the Strait of Malacca, Vietnam and the China Sea (A. mamillata) should be taken with caution.

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Use of Juvenal Plumage in Diagnosing Species Limits: An Example Using Buntings in the Genus Plectrophenax

The Auk ◽

10.1093/auk/124.3.907 ◽

2007 ◽

Vol 124 (3) ◽

pp. 907-915

Author(s):

James M. Maley ◽

Kevin Winker

Keyword(s):

Gene Flow ◽

Sexual Dimorphism ◽

Discriminant Analysis ◽

Relative Magnitude ◽

The Body ◽

Limited Evidence ◽

Species Limits ◽

Snow Bunting ◽

Conservative Nature ◽

The Difference

Abstract Species limits in the genus Plectrophenax have been difficult to assess. McKay’s Buntings (Plectrophenax hyperboreus) are very similar both morphologically and behaviorally to Snow Buntings (P. nivalis). However, their breeding ranges are allopatric, and there is limited evidence of gene flow. The juvenal plumage of McKay’s Buntings has never been described as different from that of Snow Buntings. Comparison of a series of McKay’s Buntings in juvenal plumage with a series of Snow Buntings in juvenal plumage showed clear differences between the two forms. We used color spectrophotometry to quantify the differences between the two taxa in two areas of the body that appeared to be consistently different, the throat and back. The relative magnitude of the difference between McKay’s and Snow buntings was greater than homologous differences between two subspecies of Snow Bunting (P. n. nivalis and P. n. townsendi). Four out of six variables were significantly different between McKay’s and Snow buntings, whereas none of the variables were significantly different between the two subspecies of Snow Bunting. Bonferroni corrected t-tests of sexual dimorphism and regression of the variables against year of collection showed that these factors were not associated with these differences. Discriminant analysis accurately separated 100% of the specimens into their respective groups. These differences are notable given the evolutionarily conservative nature of juvenal plumage. Our results support continued recognition of McKay’s Bunting as a species and reconfirm the use of juvenal plumage to help determine species limits. Uso del Plumaje Juvenil para Diagnosticar los Límites entre Especies: un Ejemplo en el Género Plectrophenax

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The genomic revolution and species delimitation in birds (and other organisms): gene flow matters, but what about other evolutionary forces?

10.32942/osf.io/s3dhk ◽

2020 ◽

Cited By ~ 1

Author(s):

Carlos Daniel Cadena ◽

Felipe Zapata

Keyword(s):

Gene Flow ◽

Phenotypic Variation ◽

Species Delimitation ◽

Population Level ◽

Species Limits ◽

Evolutionary Forces ◽

Species Population ◽

Genome Wide Data ◽

Evolutionary Lineages

Given the notion that species are population-level lineages and the availability of genomic data to identify separately evolving populations, researchers usually establish species limits based on gene flow or lack thereof. A strict focus on gene flow as the main –or only– criterion to delimit species involves two main complications in practice. First, approaches often used to apply this criterion to genome-wide data cannot by themselves distinguish species limits from within-species population structure, particularly in allopatric organisms. Second, recognizing as species only those lineages one can identify using such approaches fails to embrace the role of other evolutionary forces (i.e. various forms of selection) in defining evolutionary lineages. Using examples from various groups of birds, we call for the importance of considering evolutionary forces additional to gene flow in species delimitation and explain why genomic approaches commonly used in taxonomic studies may be insufficient by themselves to properly uncover species limits. By considering the processes that structure genotypic and phenotypic variation during speciation, we argue that rigorous analyses of phenotypic variation remain crucial for species delimitation in the genomics era because phenotypes uniquely inform us about the role of selection maintaining the cohesion of evolutionary lineages. Evolutionary theory describing the roles of gene flow, genetic drift and natural selection in the origin and maintenance of species calls for an integration of genomics with phenomics in avian species delimitation.

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Species limits, gene flow and host relationships of Bemisia tabaci (Hemiptera: Aleyrodidae) whitefly populations in Australia

10.14264/uql.2020.1031 ◽

2020 ◽

Author(s):

Wanaporn Wongnikong

Keyword(s):

Gene Flow ◽

Bemisia Tabaci ◽

Species Limits ◽

Host Relationships

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An overview of speciation and species limits in birds

The Auk ◽

10.1093/ornithology/ukab006 ◽

2021 ◽

Author(s):

Kevin Winker

Keyword(s):

Gene Flow ◽

Integrative Taxonomy ◽

Difficult Problem ◽

Biological Species ◽

Biological Species Concept ◽

Species Limits ◽

Main Driver ◽

Data Signal ◽

Clear Line ◽

Silver Bullet

Abstract Accurately determining avian species limits has been a challenge and a work in progress for most of a century. It is a fascinating but difficult problem. Under the biological species concept, only lineages that remain essentially independent when they are in sympatry are clearly species. Otherwise, there is no clear line yet found that marks when a pair of diverging lineages (e.g., in allopatry) become different enough to warrant full biological species status. Also, with more data, species limits often require reevaluation. The process of divergence and speciation is itself very complex and is the focus of intense research. Translating what we understand of that process into taxonomic names can be challenging. A series of issues are important. Single-locus criteria are unlikely to be convincing. Genetic independence is not a species limits requirement, but the degree of independence (gene flow) needs to be considered when there is opportunity for gene flow and independence is not complete. Time-based species (limits determined by time of separation) are unsatisfactory, though integrating time more effectively into our datasets is warranted. We need to disentangle data signal due to neutral processes vs. selection and prioritize the latter as the main driver of speciation. Assortative mating is also not likely to be an adequate criterion for determining species limits. Hybridization and gene flow are more important than ever, and there is a condition not being treated evenly in taxonomy: evolutionary trysts of 2 or more lineages stuck together through gene flow just short of speciation over long periods. Comparative methods that use what occurs between good species in contact to infer species limits among allopatric forms remain the gold standard, but they can be inaccurate and controversial. Species-level taxonomy in birds is likely to remain unsettled for some time. While the study of avian speciation has never been more exciting and dynamic, there is no silver bullet for species delimitation, nor is it likely that there will ever be one. Careful work using integrative taxonomy in a comparative framework is the most promising way forward.

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An examination of species limits in theAulacorhynchus“prasinus” toucanet complex (Aves: Ramphastidae)

PeerJ ◽

10.7717/peerj.2381 ◽

2016 ◽

Vol 4 ◽

pp. e2381 ◽

Cited By ~ 2

Author(s):

Kevin Winker

Keyword(s):

Gene Flow ◽

Natural Selection ◽

South America ◽

Multivariate Analyses ◽

Biological Species ◽

Past Century ◽

Social Selection ◽

Species Limits ◽

Color Changes ◽

The Past

The number of species recognized inAulacorhynchustoucanets has varied tremendously over the past century. Revisors seem to disagree on whether head and bill coloration are useful indicators of species limits, especially in theA.“prasinus” complex. Using morphometrics, I tested the hypothesis that the major color-based subspecific groups ofA.“prasinus”sensu latoare simply “cookie-cutter” (i.e., morphologically nearly identical) toucanets with different head and bill colorations. Univariate and multivariate analyses show that they are not simply morphological replicates of different colors: a complex array of morphometric similarities and dissimilarities occur between the major subspecific groups, and these variations differ between the sexes. Latitude and longitude had a small but significant association with female (but not male) PC1 and PC2. Hybridization and intergradation were also considered using plumage and bill characters as a surrogate to infer gene flow. Hybridization as indicated by phenotype appears to be substantial betweenA. “p.” cyanolaemusandA. “p.” atrogularisand nonexistent between other major groups, although from genetic evidence it is likely rare betweenA. “p.” albivittaandA. “p.” cyanolaemus. The congruence and complexities of the morphological and color changes occurring among these groups suggest that ecological adaptation (through natural selection) and social selection have co-occurred among these groups and that species limits are involved. Further, hybridization is not evident at key places, despite in many cases (hypothetical) opportunity for gene flow. Consequently, I recommend that this complex be recognized as comprising five biological species:A. wagleri, prasinus, caeruleogularis, albivitta,andatrogularis. Four of these also have valid subspecies within them, and additional work may eventually support elevation of some of these subspecies to full species. Species limits in South America especially need more study.

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Great Wall blocks gene flow

Nature ◽

10.1038/news030414-3 ◽

2003 ◽

Author(s):

HelenR. Pilcher

Keyword(s):

Gene Flow ◽

Great Wall

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Joseph Sidebotham: vicissitudes of a Victorian collector

Archives of Natural History ◽

10.3366/anh.2015.0305 ◽

2015 ◽

Vol 42 (2) ◽

pp. 197-210 ◽

Cited By ~ 1

Author(s):

Laurence M. Cook

Keyword(s):

Natural History ◽

Species Limits ◽

Clear Cut ◽

Natural History Collections ◽

As Species ◽

Scientific World

Joseph Sidebotham (1824–1885) was a Manchester cotton baron whose natural history collections are now in the Manchester Museum. In addition to collecting he suggested a method for identifying and classifying Lepidoptera and investigated variation within species as well as species limits. With three close collaborators, he is credited with discovering many species new to Britain in both Lepidoptera and Coleoptera. A suspicion of fraud attaches to these claims. The evidence is not clear-cut in the Lepidoptera, but a possible reason is suggested why Sidebotham, as an amateur in the increasingly professional scientific world, might have engaged in deceit.

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Differentiation and Interrelations of Two Representatives of Laudakia stellio Complex (Reptilia: Agamidae) in Israel

Russian Journal of Herpetology ◽

10.30906/1026-2296-1997-4-2-102-114 ◽

2011 ◽

Vol 4 (2) ◽

pp. 102-114 ◽

Cited By ~ 2

Author(s):

Evgenyi N. Panov ◽

Larissa Yu. Zykova

Keyword(s):

Population Structure ◽

Gene Flow ◽

Habitat Preference ◽

Additional Data ◽

Near East ◽

Field Studies ◽

Subspecies Level ◽

Limited Gene Flow ◽

Study Sites ◽

And Behavior

Field studies were conducted in Central Negev within the breeding range of Laudakia stellio brachydactyla and in NE Israel (Qyriat Shemona) in the range of an unnamed form (tentatively “Near-East Rock Agama”), during March – May 1996. Additional data have been collected in Jerusalem at a distance of ca. 110 km from the first and about 170 km from the second study sites. A total of 63 individuals were caught and examined. The animals were marked and their subsequent movements were followed. Social and signal behavior of both forms were described and compared. Lizards from Negev and Qyriat Shemona differ from each other sharply in external morphology, habitat preference, population structure, and behavior. The differences obviously exceed the subspecies level. At the same time, the lizards from Jerusalem tend to be intermediate morphologically between those from both above-named localities, which permits admitting the existence of a limited gene flow between lizard populations of Negev and northern Israel. The lizards from NE Israel apparently do not belong to the nominate subspecies of L. stellio and should be regarded as one more subspecies within the species.

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