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Background: In the speciation continuum the strength of reproductive isolation varies, and species boundaries are blurred by gene flow. Interbreeding among giraffe (Giraffa spp.) in captivity is known and anecdotal reports of natural hybrids exist. In Kenya, Nubian (G. camelopardalis camelopardalis), reticulated (G. reticulata), and Masai giraffe sensu stricto (G. tippelskirchi tippelskirchi) are parapatric, and thus the country might be a melting pot for these taxa. We analyzed 128 genomes of wild giraffe, 113 newly sequenced, representing these three taxa.
Results: We found varying levels of Nubian ancestry in 13 reticulated giraffe sampled across the Laikipia Plateau most likely reflecting historical gene flow between these two lineages. Although comparatively weaker signs of ancestral gene flow and potential mitochondrial introgression from reticulated into Masai giraffe were also detected, estimated admixture levels between these two lineages are minimal. Importantly, contemporary gene flow between East African giraffe lineages was not statistically significant. Effective population sizes have declined since the Late Pleistocene, more severely for Nubian and reticulated giraffe.
Conclusions: Despite historically hybridizing, these three giraffe lineages have maintained their overall genomic integrity suggesting effective reproductive isolation, consistent with the previous classification of giraffe into four species.
A century and a half since the time of Hewitson, we are experiencing a renaissance in species discovery fueled by whole genome sequencing. A large-scale genomic analysis of Hesperiidae Latreille, 1809 (Lepidoptera), including primary type specimens, reveals a deluge of species new to science. One hundred of them (one in a new genus) are described here from the New World (type localities are given in parenthesis): Drephalys (Drephalys) diovalis Grishin, new species (Ecuador: Napo), Euriphellus panador Grishin, new species (Ecuador: Esmeraldas), Euriphellus panamicus Grishin, new species (Panama: Panama), Cecropterus (Thorybes) viridissimus Grishin, new species (Ecuador: Zamora-Chinchipe), Cecropterus (Murgaria) dariensis Grishin, new species (Panama: Darien), Urbanus (Urbanus) mericuti Grishin, new species (Ecuador: Napo), Telegonus (Telegonus) pastus Grishin, new species (Panama: Panama), Autochton (Autochton) dora Grishin, new species (Ecuador: Pastaza), Astraptes centralis Grishin, new species (Panama: Colón), Aguna claxonica Grishin, new species (Ecuador: Napo), Aguna esmeralda Grishin, new species (Ecuador: Esmeraldas), Aguna lata Grishin, new species (Guyana), Ridens angulinea Grishin, new species (Peru: Cuzco), Pythonides lera Grishin, new species (Peru: Cuzco), Pythonides latemarginatus Grishin, new species (Panama: Panama), Gindanes variegatus Grishin, new species (Brazil: Mato Grosso), Milanion (Milanion) virga Grishin, new species (Brazil: Rondônia), Milanion (Milanion) furvus Grishin, new species (Panama: Panama), Milanion (Milanion) laricus Grishin, new species (Ecuador: Napo), Charidia ronda Grishin, new species (Brazil: Rondônia), Pseudodrephalys tinas Grishin, new species (Peru: Loreto), Pseudodrephalys argus Grishin, new species (Suriname: Para), Achlyodes calvus Grishin, new species (Brazil: Santa Catarina), Spioniades artemis Grishin, new species (Panama: Panama), Spioniades artemidoides Grishin, new species (Brazil: Santa Catarina), Myrinia orieca Grishin, new species (Ecuador: Orellana), Myrinia aragua Grishin, new species (Venezuela: Aragua), Myrinia maculosa Grishin, new species (Guatemala), Myrinia manchada Grishin, new species (Guyana), Polyctor (Fenops) lamperus Grishin, new species (Panama: Darien), Nisoniades (Nisoniades) lutum Grishin, new species (Mexico: Guerrero. ), Bolla (Stolla) vena Grishin, new species (Venezuela: Aragua), Staphylus (Vulga) vula Grishin, new species (Mexico: Veracruz), Staphylus (Vulga) vulga Grishin, new species (Panama: Darien), Staphylus (Staphylus) rotundalus Grishin, new species (Ecuador: Napo), Staphylus (Staphylus) yucatanus Grishin, new species (Mexico: Quintana Roo/Yucatan), Heliopetes (Heliopetes) lana Grishin, new species (Guatemala), Canesia ella Grishin, new species (Venezuela: Barinas), Paches (Paches) loxeca Grishin, new species (Ecuador: Morona-Santiago), Clito congruens Grishin, new species (Panama: Colón), Cycloglypha corax Grishin, new species (Brazil: Rio de Janeiro), Festivia peruvia Grishin, new species (Peru: Huánuco), Decinea notata Grishin, new species (Ecuador: Napo), Pompeius fuscus Grishin, new species (Brazil: Minas Gerais), Vernia clara Grishin, new species (Panama: Chiriquí), Oligoria (Oligoria) obtena Grishin, new species (Ecuador: Napo), Thespieus mandal Grishin, new species (Brazil: Rio de Janeiro), Psoralis (Saniba) magnamacus Grishin, new species (Panama: Darien), Alychna ayonis Grishin, new species (Ecuador: Napo), Wahydra banios Grishin, new species (Ecuador: Tungurahua), Wahydra cuzcona Grishin, new species (Peru: Cuzco), Cynea (Cynea) aureofimbra Grishin, new species (Ecuador), Cynea (Nycea) quada Grishin, new species (Ecuador: Napo), Cynea (Quinta) achirae Grishin, new species (Mexico: Tamaulipas), Eutus amazonicus Grishin, new species (Peru: Madre de Dios), Eutus incus Grishin, new species (Peru: Cuzco), Eutus septemaculatus Grishin, new species (Brazil: Mato Grosso), Godmia viridicapita Grishin, new species (Ecuador: Napo), Rhomba pulla Grishin, new species (Peru: Cuzco), Niconiades victoria Grishin, new species (Mexico: Tamaulipas), Lancephallus purpurus Grishin, new genus and new species (Guyana), Mnasicles (Remella) ecua Grishin, new species (Ecuador: Pichincha), Amblyscirtes (Amblyscirtes) aeratus Grishin, new species (Mexico: Oaxaca), Amblyscirtes (Mastor) chrysoplea Grishin, new species (Mexico: Oaxaca), Amblyscirtes (Mastor) chrysomisa Grishin, new species (Mexico: Chiapas), Amblyscirtes (Flor) meridus Grishin, new species (Mexico: Veracruz), Rectava chiriquensis Grishin, new species (Panama: Chiriquí), Cobalopsis adictys Grishin, new species (Panama: Veraguas), Cymaenes melaporphyrus Grishin, new species (Mexico: San Luis Potosí), Lerema (Morys) ecuadorica Grishin, new species (Ecuador: Pichincha), Saturnus obscurior Grishin, new species (Panama: Darien), Cantha zoirodicta Grishin, new species (Peru: Madre de Dios), Cantha meiodicta Grishin, new species (Peru: Madre de Dios), Phlebodes duplex Grishin, new species (Guatemala: Cayuga), Lychnuchus (Enosis) valle Grishin, new species (Colombia: Valle), Eutychide ochoides Grishin, new species (Peru: Cuzco), Dion bora Grishin, new species (Panama: Darien), Dion occida Grishin, new species (Peru: Madre de Dios), Eprius (Eprius) veledinus Grishin, new species (Ecuador: Pichincha), Radiatus panamensis Grishin, new species (Panama: Panama), Pheraeus pulcher Grishin, new species (Peru: Madre de Dios), Callimormus rades Grishin, new species (Panama: Panama), Gubrus lubens Grishin, new species (Ecuador: Loja), Ludens labens Grishin, new species (Panama: Darien), Rigga isa Grishin, new species (Ecuador: Napo), Flaccilla lactea Grishin, new species (Peru: Cuzco), Falga athena Grishin, new species (Panama: Darien), Panoquina jay Grishin, new species (Peru: Loreto), Calpodes salianus Grishin, new species (Peru: Madre de Dios), Calpodes stingo Grishin, new species (Ecuador: Sucumbíos), Aides nobra Grishin, new species (Panama: Colón), Thracides pavo Grishin, new species (Mexico: Tabasco), Talides eluta Grishin, new species (Peru: Cuzco), Talides laeta Grishin, new species (Peru: Cuzco), Neoxeniades angustior Grishin, new species (Brazil: Rio de Janeiro), Damas zea Grishin, new species (Guyana), Tromba xantha Grishin, new species (Mexico: Veracruz), Perichares fura Grishin, new species (Ecuador: Pichincha), Carystoides (Balma) goliath Grishin, new species (Colombia: Valle), and Agathymus galeana Grishin, new species (Mexico: Nuevo Leon). Additionally, we present evidence to support 22 taxa as species (not subspecies or synonyms) and synonymize one genus and four species. Namely, the following taxa are species: Milanion pilta Evans, 1953 (not Milanion pilumnus Mabille and Boullet, 1917), Milanion latior Mabille and Boullet, 1917 (not a synonym of Milanion marciana Godman and Salvin, 1895), Charidia pilea Evans, 1953, and Charidia pocus Evans, 1953 (not Charidia lucaria (Hewitson, 1868)), Paches (Paches) gloriosus Röber, 1925 and Paches (Paches) loxana Evans, 1953 (not Paches (Paches) loxus (Westwood, 1852)), Spioniades anta Evans, 1953 (not Spioniades abbreviata (Mabille, 1888)), Decinea onasima (Hewitson, 1877) and Decinea formosus (Hayward, 1940) (not Decinea dama (Herrich-Schäffer, 1869)), Thespieus guerreronis (Dyar, 1913) (not Thespieus dalman (Latreille, [1824])), Cynea (Nycea) erebina (Möschler, 1879) and Cynea (Nycea) cleochares (Mabille, 1891) (not Cynea (Cynea) diluta (Herrich-Schäffer, 1869)), Amblyscirtes (Mastor) repta Evans, 1955 (not Amblyscirtes (Flor) florus (Godman, 1900)), Saturnus tiberius (Möschler, 1883), Saturnus conspicuus (E. Bell, 1941), Saturnus meton (Mabille, 1891), and Saturnus obscurus (E. Bell, 1941) (not Saturnus reticulata (Plötz, 1883)), Phlebodes sifax Evans, 1955 (not Phlebodes campo (E. Bell, 1947)), Eutychide ochus Godman, 1900 and Eutychide rogersi (Kaye, 1914) (not a subspecies and a synonym, respectively, of Eutychide subcordata (Herrich-Schäffer, 1869)), Falga mirabilis Evans, 1955, Falga jacta Evans, 1955, and Falga ombra Evans, 1955 (not Falga jeconia (A. Butler, 1870)); and the following taxa are junior subjective synonyms: Libra Evans, 1955 (of Phemiades Hübner, [1819]), Papilio clito Fabricius, 1787 of Milanion hemes hemes (Cramer, 1777), Pamphila hycsos Mabille, 1891 of Cynea (Nycea) erebina (Möschler, 1879), Hesperia olympia Plötz, 1882 of Eutychide subcordata (Herrich-Schäffer, 1869), and Hesperia ocrinus Plötz, 1882 of Aides aegita (Hewitson, 1866). Furthermore, we propose new combinations for genus-species: Lychnuchus (Enosis) ponka (Evans, 1955) (not Thoon Godman, 1900), and species-subspecies: Charidia pocus mayo Evans, 1953 (not Charidia lucaria (Hewitson, 1868)), Decinea onasima boliviensis (E. Bell, 1930) (not Decinea dama (Herrich-Schäffer, 1869)), Cynea (Nycea) erebina somba Evans, 1955 (not Pamphila hycsos Mabille, 1891), Saturnus tiberius suffuscus (Hayward, 1940) (not Saturnus reticulata (Plötz, 1883)), and Falga mirabilis odol Evans, 1955 (not Falga jeconia (A. Butler, 1870)). Then, Milanion pilumnus var. hemestinus Mabille and Boullet, 1917 is a junior subjective synonym of Milanion pilumnus pilumnus Mabille and Boullet, 1917, not of Milanion leucaspis (Mabille, 1878). Lectotypes are designated for nine taxa (names in original combinations below): Pellicia bromias Godman and Salvin, 1894 (Mexico: Veracruz, Atoyac), Nisoniades perforata Möschler, 1879 (Colombia), Helias ascalaphus Staudinger, 1876 (central Panama), Pamphila hycsos Mabille, 1891 (Colombia), Amblyscirtes fluonia Godman, 1900 (Mexico: Guerrero, Xocomanatlan), Mastor anubis Godman, 1900 (Mexico: Guerrero, Omiltemi), Eutychide ochus Godman, 1900 (Mexico: Veracruz, Atoyac), Cobalus subcordata Herrich-Schäffer, 1869 (Southeast Brazil), and Thracides xanthura Godman, 1901 (Panama: Chiriquí Province, Bugaba). A neotype is designated for Eudamus briccius Plötz, 1881 (Guyana: Iwokrama Forest).
ZooBank registration. urn:lsid:zoobank.org:pub:ACDF923B-906D-460E-9707-259E0ECDBCA8
Species is the fundamental taxonomic unit in biology and its delimitation has implications for conservation. In giraffe (Giraffa spp.), multiple taxonomic classifications have been proposed since the early 1900s.1 However, one species with nine subspecies has been generally accepted,2 likely due to limited in-depth assessments, subspecies hybridizing in captivity,3,4 and anecdotal reports of hybrids in the wild.5 Giraffe taxonomy received new attention after population genetic studies using traditional genetic markers suggested at least four species.6,7 This view has been met with controversy,8 setting the stage for debate.9,10 Genomics is significantly enhancing our understanding of biodiversity and speciation relative to traditional genetic approaches and thus has important implications for species delineation and conservation.11 We present a high-quality de novo genome assembly of the critically endangered Kordofan giraffe (G. camelopardalis antiquorum)12 and a comprehensive whole-genome analysis of 50 giraffe representing all traditionally recognized subspecies. Population structure and phylogenomic analyses support four separately evolving giraffe lineages, which diverged 230–370 ka ago. These lineages underwent distinct demographic histories and show different levels of heterozygosity and inbreeding. Our results strengthen previous findings of limited gene flow and admixture among putative giraffe species6,7,9 and establish a genomic foundation for recognizing four species and seven subspecies, the latter of which should be considered as evolutionary significant units. Achieving a consensus over the number of species and subspecies in giraffe is essential for adequately assessing their threat level and will improve conservation efforts for these iconic taxa.
Analyses of whole genomic shotgun datasets, COI barcodes, morphology, and historical literature suggest that the following 13 butterfly species from the family Hesperiidae (Lepidoptera: Papilionoidea) in Texas, USA are distinct from their closest named relatives and therefore are described as new (type localities are given in parenthesis): Spicauda atelis Grishin, new species (Hidalgo Co., Mission), Urbanus (Urbanus) rickardi Grishin, new species (Hidalgo Co., nr. Madero), Urbanus (Urbanus) oplerorum Grishin, new species (Hidalgo Co., Mission/Madero), Telegonus tsongae Grishin, new species (Starr Co., Roma), Autochton caballo Grishin, new species (Hidalgo Co., 6 mi W of Hidalgo), Epargyreus fractigutta Grishin, new species (Hidalgo Co., McAllen), Aguna mcguirei Grishin, new species (Cameron Co., Brownsville), Polygonus pardus Grishin, new species (Hidalgo Co., McAllen), Arteurotia artistella Grishin, new species (Hidalgo Co., Mission), Heliopetes elonmuski Grishin, new species (Cameron Co., Boca Chica), Hesperia balcones Grishin, new species (Travis Co., Volente), Troyus fabulosus Grishin, new species (Hidalgo Co., Peñitas), and Lerema ochrius Grishin, new species (Hidalgo Co., nr. Relampago). Most of these species are known in the US almost exclusively from the Lower Rio Grande Valley in Texas. Nine of the holotypes were collected in 1971-1975, a banner period for butterfly species newly recorded from the Rio Grande Valley of Texas; five of them collected by William W. McGuire, and one by Nadine M. McGuire. At the time, these new species have been recorded under the names of their close relatives. A Neotype is designated for Papilio fulminator Sepp, [1841] (Suriname). Lectotypes are designated for Goniurus teleus Hübner, 1821 (unknown, likely in South America), Goniloba azul Reakirt, [1867] (Mexico: Veracruz) and Eudamus misitra Plötz, 1881 (Mexico). Several taxonomic changes are proposed. The following taxa are species (not subspecies): Spicauda zalanthus (Plötz, 1880), reinstated status (not Spicauda teleus (Hübner, 1821)), Telegonus fulminator (Sepp, [1841]), reinstated status (not Telegonus fulgerator (Walch, 1775), Telegonus misitra (Plötz, 1881), reinstated status (not Telegonus azul (Reakirt, [1867])), Autochton reducta (Mabille and Boullet, 1919), new status (not Autochton potrillo (Lucas, 1857)), Epargyreus gaumeri Godman and Salvin, 1893, reinstated status (not Epargyreus clavicornis (Herrich-Schäffer, 1869)), and Polygonus punctus E. Bell and W. Comstock, 1948, new status (not Polygonus savigny (Latreille, [1824])). Urbanus ehakernae Burns, 2014 and Epargyreus socus chota Evans, 1952 are junior subjective synonyms of Urbanus alva Evans, 1952 and Epargyreus clavicornis (Herrich-Schäffer, 1869), respectively, and Epargyreus gaumeri tenda Evans, 1955, new combination is not a subspecies of E. clavicornis.
ZooBank registration. https://zoobank.org/D5462F9E-E08D-46C6-898D-76EE7466DD19
Downy mildews caused by obligate biotrophic oomycetes result in severe crop losses worldwide. Among these pathogens, Pseudoperonospora cubensis and P. humuli, two closely related oomycetes, adversely affect cucurbits and hop, respectively. Discordant hypotheses concerning their taxonomic relationships have been proposed based on host–pathogen interactions and specificity evidence and gene sequences of a few individuals, but population genetics evidence supporting these scenarios is missing. Furthermore, nuclear and mitochondrial regions of both pathogens have been analyzed using microsatellites and phylogenetically informative molecular markers, but extensive comparative population genetics research has not been done. Here, we genotyped 138 current and historical herbarium specimens of those two taxa using microsatellites (SSRs). Our goals were to assess genetic diversity and spatial distribution, to infer the evolutionary history of P. cubensis and P. humuli, and to visualize genome-scale organizational relationship between both pathogens. High genetic diversity, modest gene flow, and presence of population structure, particularly in P. cubensis, were observed. When tested for cross-amplification, 20 out of 27 P. cubensis-derived gSSRs cross-amplified DNA of P. humuli individuals, but few amplified DNA of downy mildew pathogens from related genera. Collectively, our analyses provided a definite argument for the hypothesis that both pathogens are distinct species, and suggested further speciation in the P. cubensis complex.
Abstract
Divergence is mostly viewed as a progressive process often initiated by selection targeting individual loci, ultimately resulting in ever increasing genomic isolation due to linkage. However, recent studies show that this process may stall at intermediate stable equilibrium states without achieving complete genomic isolation. We tested the extent of genomic isolation between two recurrently hybridizing nonbiting midge sister taxa, Chironomus riparius and Chironomus piger, by analyzing the divergence landscape. Using a principal component‐based method, we estimated that only about 28.44% of the genomes were mutually isolated, whereas the rest was still exchanged. The divergence landscape was fragmented into isolated regions of on average 30 kb, distributed throughout the genome. Selection and divergence time strongly influenced lengths of isolated regions, whereas local recombination rate only had minor impact. Comparison of divergence time distributions obtained from several coalescence‐simulated divergence scenarios with the observed divergence time estimates in an approximate Bayesian computation framework favored a short and concluded divergence event in the past. Most divergence happened during a short time span about 4.5 million generations ago, followed by a stable equilibrium between mutual gene flow through ongoing hybridization for the larger part of the genome and isolation in some regions due to rapid purifying selection of introgression, supported by high effective population sizes and recombination rates.
Impact Summary
The process of speciation has fascinated biologists from early on. Prevailing theory suggested that gene flow among populations is the main obstacle for their divergence. Recently, it became clear that speciation with gene flow is possible under certain circumstances. However, it remains unclear how the divergence process proceeds in time, how widespread the phenomenon is, and whether it always and inevitably leads to complete isolation. Comparing the genomes of individuals of two regularly hybridizing sister taxa of nonbiting midges, we could show that they diverged during a short period millions of generations ago. Their divergence process apparently ceased before the entire genome was mutually isolated. The taxa remain distinct since, even though they share most of their genome. Our findings thus extend our view of the nature of species and the temporal dynamics of their divergence and describe novel approaches to analyze both current and past divergence processes.
All giraffe (Giraffa) were previously assigned to a single species (G. camelopardalis) and nine subspecies. However, multi‐locus analyses of all subspecies have shown that there are four genetically distinct clades and suggest four giraffe species. This conclusion might not be fully accepted due to limited data and lack of explicit gene flow analyses. Here, we present an extended study based on 21 independent nuclear loci from 137 individuals. Explicit gene flow analyses identify less than one migrant per generation, including between the closely related northern and reticulated giraffe. Thus, gene flow analyses and population genetics of the extended dataset confirm four genetically distinct giraffe clades and support four independent giraffe species. The new findings support a revision of the IUCN classification of giraffe taxonomy. Three of the four species are threatened with extinction, and mostly occurring in politically unstable regions, and as such, require the highest conservation support possible.
Evolutionary developmental biology (evo-devo) suggests a distinction between modular and systemic variation. In the case of modular change, the conservation of the overall structure helps recognizing affinities, while a single, fast evolving module is likely to produce a bonanza for the taxonomist, while systemic changes produce strongly deviating morphologies that cause problems in tracing homologies. Similarly, changes affecting the whole life cycle are more challenging than those limited to one stage. Developmental modularity is a precondition for heterochrony. Analyzing a matrix of morphological data for paedomorphic taxa requires special care. It is, however, possible to extract phylogenetic signal from heterochronic patterns. The taxonomist should pay attention to the intricacies of the genotype→phenotype map. When using genetic data to infer phylogeny, a comparison of gene sequences is just a first step. To bridge the gap between genes and morphology we should consider the spatial and temporal patterns of gene expression, and their regulation. Minor genetic change can have major phenotypic effects, sometimes suggesting saltational evolution. Evo-devo is also relevant in respect to speciation: changes in developmental schedules are often implicated in the divergence between sympatric morphs, and a developmental modulation of ‘temporal phenotypes’ appears to be responsible for many cases of speciation.