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Illuminating the obscured phylogenetic radiation of South American Sylvilagus Gray, 1867 (Lagomorpha: Leporidae)
Abstract
Largely shallow and putatively explosive divergences in the family Leporidae (rabbits and hares; order: Lagomorpha) have resulted in phylogenetic relationships that remain currently unresolved. These rapid radiations in different branches of the leporid tree have resulted in conflicting phylogenetic hypotheses. However, this phylogenetic incongruence may also result from inadequate taxon or character sampling, due to the high number of extinct and difficult to sample extant species, and highly conserved morphological characters. Sylvilagus (cottontail rabbits) constitute about 30% of the known extant leporid species. New species are routinely being recognized, and phylogenetic relationships with respect to other leporid genera, and within the genus, have failed to be recovered with certainty. Within Sylvilagus, the South American S. brasiliensis is the most widespread and poorly known taxon, likely comprising multiple species. Here, we reanalyze previously published moleculardata from phylogenetic studies on Leporidae, focusing on the S. brasiliensis group, and assessing phylogenetic relationships using bifurcating trees and split networks to identify phylogenetic regions with polytomies. We estimate differentiation and phylogenetic relationships of molecular lineages within the S. brasiliensis group. Our analyses suggest that this group contains a number of divergent taxa, well differentiated from other cottontail species. We discern two major polytomies during leporid diversification. The first, at the base of the leporid radiation, likely resulted from a combination of hard (rapid radiation) and soft polytomies (high number of unsampled extinct species). The second polytomy likely resulted from a rapid radiation during the initial diversification of the genus Sylvilagus. We conclude that only a molecular phylogeny based on a broader taxonomic representation will fully resolve leporid phylogeny.
... Halanych and Robinson (1999), based on 12S rDNA data, estimated the divergence between the European rabbit, Oryctolagus Lilljeborg, 1874 andLepus Linnaeus, 1758 (hares andjackrabbits) at between approximately 16 and 12 Ma. In contrast, Su and Nei (1999) advocated for a divergence at 21.9 ± 3.8 Ma and considered the late Miocene as the critical time period in this cladogenesis (Ge et al. 2015), with the appearance of the extinct leporine †Alilepus (Dice, 1931) hypothesized to have occurred by means of rapid radiations (Halanych and Robinson 1999;Robinson and Matthee 2005;Flynn et al. 2014;Silva et al. 2019). ...
... With respect to Leporidae, they concluded that Pronolagus was the basalmost taxon. Silva et al. (2019) analyzed newly generated as well as previously published molecular data from leporids (from Matthee et al. 2004), focusing on the relationships among Sylvilagus species, using bifurcating trees and split networks with the aim of identifying phylogenetic regions with polytomies. Those authors concluded that a rapid radiation of leporids in general, and during the initial diversification of the genus Sylvilagus in particular, was responsible for the difficulty in elucidating clear phylogenetic relationships underlying the basal radiation of these groups. ...
... Those authors concluded that a rapid radiation of leporids in general, and during the initial diversification of the genus Sylvilagus in particular, was responsible for the difficulty in elucidating clear phylogenetic relationships underlying the basal radiation of these groups. Silva et al. (2019) found inconsistencies in the relationships among genera across analyses but showed that all leporids are included in a basal leporid polytomy. In short, obtaining a robust and resolved phylogeny has been challenging for many biological groups, most particularly those that diversified rapidly and contemporaneously (Whitfield and Lockhart 2007)like leporids, due to error sources such as substitution events (Halanych and Robinson 1999)-convergence in anatomical characteristics, absence of chromosomal synapomorphies, high levels of homoplasy in mtDNA, and the short internodes underlying explosive largely contemporaneous radiations (Matthee et al. 2004;Ge et al. 2013Ge et al. , 2015Kraatz and Sherratt 2016;Silva et al. 2019). ...
Lagomorpha (lagomorphs), the order of mammals including pikas, hares, and rabbits, is distributed on all continents. The order currently is hypothesized to comprise 12 genera and 108 species, split into two families: Ochotonidae (pikas) and Leporidae (rabbits and hares). Molecular and morphological attempts have been undertaken to resolve the phylogeny of lagomorphs, although chronological relationships are still to be established. The aim of this research was to unravel lagomorph phylogeny using ultraconserved elements. We focused on Romerolagus, in light of its largely unknown phylogenetic relationships and sparse fossil record, to assess times of divergence for the genus. We obtained samples from at least one species in each of 11 genera (except Caprolagus) comprising the order and captured and sequenced ultraconserved elements (UCEs). A Maximum-Likelihood phylogenetic analysis was carried out on the 4,195 loci captured, resulting in 59,112 informative sites. We further used BEAST2 v2.6.3 on the CIPRES computing cluster to estimate the timing of cladogenesis in lagomorph evolution. Our results confirm that lagomorphs and rodents split about 65 million years ago. The former further split into its constituent families, Leporidae and Ochotonidae, about 60 million years ago. Pronolagus rupestris and Nesolagus timminsi were retrieved as basal sister taxa; the most recent common ancestor of that clade and remaining leporids was estimated to have existed about 47 million years ago. Romerolagus diazi is sister to remaining Leporidae excluding Pronolagus and Nesolagus, a topology that generally matches previously published phylogenies, although our results suggest a most recent common ancestor of Romerolagus and remaining ingroup leporids at ca. 4.8 Ma (95% highest posterior density [HPD] interval: 5.9-3.8 Ma), with an internal diversification in the Middle to Late Pleistocene (0.9 Ma; 95% HPD 1.8-0.2 Ma). Our final results yielded a robust phylogeny with high support values for every clade of the order Lagomorpha and unraveled previously unresolved phylogenetic relationships. In addition, we further conclude that the method we used, UCEs, may serve to complete the entire phylogeny of mammals by using existing museum specimens.
... Sylvilagus dicei obtains as the immediate sister taxon to the composite S. brasiliensis group, thought to be restricted to South America . This latter is represented in this study by a multispecies assemblage that formed the basis of Silva et al. (2019). The successive sister taxon to the dicei-brasiliensis clade is the S. gabbi group, which similarly displays two clades: a Caribbean clade and a North Hills clade from the hill country of northern Alajuela Province, north of the Tilar an and Central mountain ranges. ...
... Grey bars surrounding nodes represent 95% confidence intervals. Diersing & Wilson 2017;Ruedas et al. 2017Ruedas et al. , 2019Silva et al., 2019). It therefore is largely unsurprising that the taxonomic framework currently applied to Central American Sylvilagus likewise shows signs of fraying: all the major species show genetic structuring likely indicative of polytypic species complexes. ...
... In the phylogeny resulting from our genetic analysis, a monophyletic clade constituted by five individuals obtained as sister taxon to S. brasiliensis (Fig. 1), represented by a multi-taxon assemblage used by Silva et al. (2019). All samples represent highland individuals, some collected near the type locality of El Copey de Dota, Cordillera de Talamanca, San Jos e Province, Costa Rica (ca. 9 38'38"N, 83 55'16"W), at an elevation of ca. ...
Dice’s cottontail, Sylvilagus dicei, only was recognized as a valid species in 1981 after having been subsumed in synonymy with S. brasiliensis and S. gabbi, which latter also at times had been synonymized with an ill-defined and broadly distributed S. brasiliensis. Phylogenetic relationships of S. dicei remain poorly resolved, as does the distribution of the species. We collected new specimens of S. dicei and carried out phylogenetic analyses of combined cytochrome-b and 12S rRNA mitochondrial loci. Molecular data confirm the taxonomic status of S. dicei as a species and place it basal to the South American S. brasiliensis radiation; the successive sister taxon to this clade is Gabb’s cottontail, S. gabbi. Time-calibrated analyses support simultaneous internal diversification events in S. dicei and S. gabbi ∼250 KYA. The new specimens, together with literature and museum records including the holotype, enabled us to more accurately map the distribution of S. dicei. Specimens are restricted to forested uplands in Costa Rica and western Panama. Although the total altitudinally suitable area for the species is 10,313 km², removal of urban and agricultural areas not suited for its habitation result in a fragmented range of 9,115 km². Conservation threats include high predation loads from the invasive coyote, Canis latrans, urbanization, agriculture, and hunting.
... GÊNERO Sylvilagus GRAY, 1867 O gênero Sylvilagus está presente exclusivamente nas Américas, mas Sylvilagus floridanus é uma espécie invasora na Europa (Tizzani et al., 2014). São atualmente reconhecidas 20 espécies Silva et al., 2019). Segundo Dawson (2008), este gênero pode ser distinguido de outras espécies da família Leporidae pelo osso interparietal claramente distinguível e o segundo prémolar superior com duas ou três reentrâncias. ...
... Segundo Diersing (1981), as medidas externas são (n = 105): comprimento total médio de 372 mm, comprimento do corpo de 349,3 mm, comprimento da cauda de 22,2 mm, comprimento da orelha de 48,7 mm, comprimento do pé de 77,1 mm e comprimento do crânio de cerca de 70 mm. O peso é de 1150 g (Schaller, 1983 (Ruedas & Salazar-Bravo, 2007;Bonvicino et al., 2015;Ruedas et al., 2017Ruedas et al., , 2019Ruedas & Smith, 2018;Silva et al., 2019). Resumidamente, eram reconhecidas 21 subespécies de Sylvilagus brasiliensis (Hoffmann & Smith, 2005), com base em variações de coloração, comprimento e textura da pelagem. ...
Os tapitis são os únicos lagormorfos nativos da América do Sul, todos pertencendo ao gênero Sylvilagus, com 20 espécies. No Neotrópico, uma única espécie, Sylvilagus brasiliensis, com 21 sub-espécies previamente reconhecidas, foi dividida em várias espécies, entre as quais três são encontradas no Brasil, com base em dados moleculares citogenéticos e morfológicos. Sylvilagus brasiliensis sensu stricto foi geograficamente restrita ao Centro de Endemismo de Pernambuco, na região biogeográfica da Mata Atlântica, ao norte do rio São Francisco. S. tapetillus foi delimitada e restrita geograficamente à planície costeira do Rio de Janeiro. Para a espécie de Sylvilagus que ocorre no Pantanal, sugere-se manter a atribuição do nome Sylvilagus brasiliensis sensu lato, tendo em vista diferenças morfológicas cranianas importantes, com espécimes atribuíveis a S. minensis, bem como a ausência de espécimes e dados de espécimes do Pantanal, assim como de espécimes atribuíveis a S. paraguensis.
... Considerando estudos genéticos recentes (Silva et al. 2019), julgamos ser precipitada a classificação de espécimes da Gruta Cuvieri como Sylvilagus cf. brasiliensis proposta por Chahud et al. (2020). ...
... e em espécimes classificados como Sylvilagus brasiliensis minensis da região de Lagoa Santa (PaulaCouto, 1979), porém a classificação como subespécie S. b. minensis gera discussão. Baseado nissoRuedas et al. (2017) sugeriram a promoção para o nível de espécie, Sylvilagus minensis, para os espécimes das regiões ao sul e sudeste do Brasil.O gênero Sylvilagus foi analisado geneticamente porSilva et al. (2019) que observaram diferenças genéticas regionais, não apenas fenotípicas, dentro de diversas espécies e subespécies deste gênero. Importante ressaltar que espécimes de morfologia externa idêntica podem apresentar diferenciação genética e, por isso, a diferença morfológica não é suficiente para determinar espécies. ...
A Gruta Cuvieri, parte do complexo cárstico de Lagoa Santa (Minas Gerais, Brasil), preservou grande número de restos osteológicos de mamíferos. Um dos clados preservados em seus depósitos é a família Leporidae. O objetivo deste trabalho é a divulgação de novos dados atribuídos aos Leporidae encontrados na Gruta Cuvieri. O material recuperado revelou a presença de espécimes de tamanhos variados, tanto no Pleistoceno quanto no Holoceno, não sendo possível a identificação em nível de espécie. Dado o pouco conhecimento acerca da variação anatômica de fósseis e subfósseis do Quaternário brasileiro e os novos dados genéticos que apontam para uma grande diversidade no gênero Sylvilagus, sugerimos a classificação dos espécimes da Gruta Cuvieri como Sylvilagus sp..
... Here we used the concept of Marmosa demerarae (Thomas, 1905) of Silva et al. (2019a) following Quintela et al. (2020). We treated Calomys mattevii Gurgel-Filho, Feijó & Langguth 2015 as a junior synonym of C. expulsus (Lund, 1840), according to Gutiérrez & Marinho-Filho (2017); Sylvilagus minensis as a valid species based on Ruedas et al. (2017) and Silva et al. (2019b); and we did not treat Galea flavidens as valid, according to Bezerra (2008), differing from the previous checklists. The concept of Holochilus sciureus follows the recent study of Prado et al. (2021). ...
... Currently, this complex taxonomic history began to be elucidated based on phylogenetic relationships among South American populations. Ruedas et al. (2017) recognized at least three distinct species for the country: S. brasiliensis, S. minensis and S. tapetillus, with other taxonomic issues yet to be clarified (Silva et al. 2019b). In Goiás state, only S. minensis is expected to occur (Bonvicino et al. 2015;Ruedas et al. 2017). ...
The state of Goiás, in central Brazil, is covered mainly by the Cerrado domain, with the Alto Paraná Atlantic Forest occupying its central-southern portion. Goiás is one of the 20 Brazilian federative units without a mammal checklist. In this study, we provide the first checklist of mammals from Goiás state. We recorded mammal species based primarily on the analysis of specimens housed in scientific collections as well as on literature with associated voucher material. We listed 191 mammalian species belonging to 125 genera, 31 families and 10 orders, which represents 25.2% of the mammal species occurring in Brazil. The most speciose orders were Chiroptera (90 spp.), followed by Rodentia (43 spp.), Carnivora (19 spp.) and Didelphimorphia (17 spp.). The following orders accounted for a smaller portion of the state diversity: Cetartiodactyla (7 spp.), Cingulata (7 spp.), Primates (4 spp.), Pilosa (2 spp.), Lagomorpha (1 sp.), and Perissodactyla (1 sp.). A total of 28 species (14.7%), mainly represented by medium and large-sized mammals, are nationally threatened while 12 (6.3%) are globally threatened. Our results indicate great portions of the state lacking a proper survey of mammals, especially the northwestern portion. We discuss species richness, distribution and conservation status of the mammals of Goiás state in national and regional scenarios. We highlight the need for mammal inventories based on complementary survey techniques with the collection of vouchers in order to provide karyologic, molecular, morphologic, parasitologic, and ecological data. These informations are the basis for integrative studies that lead to the understanding of current mammalian richness and diversity. Indeed, knowledge on species richness distribution in the state will guide conservation strategies, especially in areas undergoing habitat loss and fragmentation, such as the central-southern portion of Goiás. © 2021, Universidade Estadual de Campinas UNICAMP. All rights reserved.
... This may reflect species' intrinsic characteristics, such as their large distribution ranges, which are assumed to make them less vulnerable to relative small-scaled anthropogenic effects (Traill et al. 2007;Flather et al. 2011), and a poor definition of their taxonomic limits, with several Neotropical taxa requiring taxonomic reassessments (e.g. Pavan et al. 2011;Ferreira et al. 2014;Silva et al. 2019). Such information is still necessary in order to define the spatial and temporal scale to detect the genetic consequences of landscape changes (Keyghobadi 2007;Cushman et al. 2012). ...
... Considering the current knowledge gaps on Amazonian mammals (e.g. Pavan et al. 2011;Ferreira et al. 2014;Silva et al. 2019), we recommend that more attention should be given to the effects of anthropogenic landscape conversion on local patterns of genetic diversity in this region. Furthermore, meta-analyses including multiple species are especially important, due to the idiosyncratic responses reported (this work; Meyer et al. 2009;Ripperger et al. 2013Ripperger et al. , 2014aLeiva-González et al. 2019). ...
Anthropogenic landscape changes resulting in habitat degradation, loss and fragmentation might decrease connectivity and effective sizes of wild populations, threatening local biodiversity. Assumed large distributions of both species and habitats have probably discouraged studies correlating altered landscapes' structure and composition to patterns of genetic diversity in the Neotropics. Yet, considering the increasingly high rates of deforestation and habitat conversion in Amazonia, investigating local and regional-scale effects of habitat conversion on Amazonian mammals is of paramount importance. Here, we use widespread, non-threatened, phyllostomid bats to understand how current forest dynamics are influencing genetic diversity patterns and functional connectivity of eastern Amazonian volant mammals. Four frugivorous species, Carollia perspicillata, Rhinophylla pumilio, Dermanura gnoma and Artibeus obscurus, were sampled across a heterogeneously fragmented region. Twelve more or less isolated rainforest remnants surrounded by urban areas, pastures, crops, secondary forests and other land uses comprise the studied landscapes, and are compared using a landscape genetics approach applied to mitochondrial DNA loci. Here, we report species-specific consequences of habitat fragmentation. Although the overall levels of genetic diversity were high, our data show that (i) population structure is heterogeneous across the altered landscapes; (ii) landscapes with higher habitat availability harbour populations with higher genetic diversity; and (iii) the populations assessed might be demographically declining.
... As the ground layer of the sclerophyllous woodland (''cerradão'') has often little or no herbaceous layer (Goodland 1971;Durigan and Ratter 2006), the interior of these woodlands may offer no or few foods for hares. Resource opportunities might be further diminished by competition with native grazers and browsers inhabiting these forests, including the Brazilian forest rabbit (Sylvilagus brasiliensis sensu lato; Silva et al. 2019) and the brocked deer (Mazama spp). Hence, forested protected areas might represent a ''barrier'' to the expansion of the European hare. ...
... A recent study, however, suggested the European hare has a great potential to create apparent competition with native herbivores (Barbar and Lambertucci 2019). Besides, based on our findings, the European hare may not spatially co-occur with the Brazilian forest rabbit (Sylvilagus brasiliensis sensu lato; Silva et al. 2019), a forest dweller species according to our recent results (Pasqualotto et al., unpublished data). However, although our data suggest that the European hare may not be a threat to the Brazilian forest rabbit, until now, there is no study specifically dedicated to assess this. ...
The European hare (Lepus europaeus) was introduced in the late 19th century in Argentina and has since rapidly expanded northwards, currently occupying the Brazilian south and southeast. Although European hare is known to be a farmland specialist in its native Europe, what habitat types or landscape features are facilitating its expansion in the Neotropics are not yet clear. Here we assessed support to the disturbance and biotic resistance hypotheses as general drivers of this invasion. We sampled with camera-traps and track surveys 205 sites in three landscapes in southeastern Brazil. We used occupancy models that corrected for both false positive and false negative errors. The disturbance hypothesis was the top-ranked (w = 0.66) with the amount of field, sugarcane, and managed forests all affecting strongly and positively hare occupancy. Support to the biotic resistance hypothesis was lower (ΔAICc = 2.14; w = 0.23) and partial, since only native forests showed a negative effect on hare occupancy. Our findings indicate that in the expansion front occupancy of this invader is mainly dictated by niche opportunities created by native habitat transformation into agricultural lands. The biotic resistance imposed by remaining native habitats seems to play a secondary role and only due to native forests. We conclude that hare geographical expansion should increase given the prominent role of Brazil as a commodity producer and exporter. Nevertheless, fomenting forested protected areas and improving adherence of rural owners to the Brazilian Forest Act, which protects forests in private rural properties, might help lessen this spread.
... To the above two sequences, we added data from and of South American species of Sylvilagus from Silva et al. (2019) to construct a mitochondrial DNA supernetwork using 12S and Cytb data sets (Appendix I). We used SplitsTree 4.14 (Huson et al. 2004;Huson and Bryant 2006) to separately construct Neighbor Joining trees from both 12S and Cytb data, because each data set had a different number of terminal taxa. ...
... Lagomorph taxonomy and systematics have entered a new age of discovery (Donoghue and Alverson 2000) wherein there still remains "a blank space of delightful mystery" (Conrad 1899) in which reside the "rainbow colors around the outer edges of human knowledge and imagination" (Nietzsche 1878). The explosive, approximately contemporaneous diversifications in Lepus and Sylvilagus (Silva et al. 2019;Upham et al., 2019) still largely shroud the basal patterns of diversification in those genera. Although many questions remain regarding the fine-scale relationships, the broad strokes are becoming illuminated. ...
A taxonomic framework for South American cottontail rabbits (Lagomorpha: Leporidae: Sylvilagus) was recently published by Diersing and Wilson (2017). Although we agree with some of its taxonomic conclusions (e.g., species status for S. apollinaris and S. fulvescens), we disagree with others. We provide herein evidence supporting S. andinus as a valid species based on morphological characters and novel molecular data. We also provide details of the morphological characters of S. apollinaris and S. fulvescens that support separating these from S. brasiliensis. We adduce data suggestive to the effect that—absent any type material—S. defilippi is at best a nomen dubium. Finally, we provide evidence in support of recognizing additional Neotropical species of Sylvilagus.
Un esquema taxonómico para los conejos sudamericanos (Lagomorpha: Leporidae: Sylvilagus) fue recientemente publicado por Diersing y Wilson (2017). Aunque estamos de acuerdo con algunas de sus conclusiones (por ejemplo: estatus de especie válida para S. apollinaris y S. fulvescens), no estamos de acuerdo con las restantes conclusiones taxonómicas. Aportamos aquí pruebas convincentes sobre la característica naturaleza de los caracteres morfológicos y moleculares de S. andinus, pruebas que esgrimimos en apoyo de la hipótesis que esta última es una especie válida, así confirmando su escisión de S. brasiliensis. Proporcionamos detalles de los caracteres morfológicos de S. apollinaris y S. fulvescens que confirman la decisión taxonómica de asimismo separarlos de S. brasiliensis. Proporcionamos datos en aditamento que indican que a falta de cualquier material tipo para S. defilippi, este nombre es en el mejor de los casos un nomen dubium. Finalmente, ofrecemos datos y evidencia apoyando nuestras decisiones de reconocer un mayor número de especies Neotropicales de Sylvilagus que previamente se conocían.
... To the above two sequences, we added data from and of South American species of Sylvilagus from Silva et al. (2019) to construct a mitochondrial DNA supernetwork using 12S and Cytb data sets (Appendix I). We used SplitsTree 4.14 (Huson et al. 2004;Huson and Bryant 2006) to separately construct Neighbor Joining trees from both 12S and Cytb data, because each data set had a different number of terminal taxa. ...
... Lagomorph taxonomy and systematics have entered a new age of discovery (Donoghue and Alverson 2000) wherein there still remains "a blank space of delightful mystery" (Conrad 1899) in which reside the "rainbow colors around the outer edges of human knowledge and imagination" (Nietzsche 1878). The explosive, approximately contemporaneous diversifications in Lepus and Sylvilagus (Silva et al. 2019;Upham et al., 2019) still largely shroud the basal patterns of diversification in those genera. Although many questions remain regarding the fine-scale relationships, the broad strokes are becoming illuminated. ...
A taxonomic framework for South American cottontail rabbits (Lagomorpha: Leporidae: Sylvilagus) was recently published by Diersing and Wilson (2017). Although we agree with some of its taxonomic conclusions (e.g., species status for S. apollinaris and S. fulvescens), we disagree with others. We provide herein evidence supporting S. andinus as a valid species based on morphological characters and novel molecular data. We also provide details of the morphological characters of S. apollinaris and S. fulvescens that support separating these from S. brasiliensis. We adduce data suggestive to the effect that-absent any type materialS. defilippi is at best a nomen dubium. Finally, we provide evidence in support of recognizing additional Neotropical species of Sylvilagus. Un esquema taxonómico para los conejos sudamericanos (Lagomorpha: Leporidae: Sylvilagus) fue recientemente publicado por Diersing y Wilson (2017). Aunque estamos de acuerdo con algunas de sus conclusiones (por ejemplo: estatus de especie válida para S. apollinaris y S. fulvescens), no estamos de acuerdo con las restantes conclusiones taxonómicas. Aportamos aquí pruebas convincentes sobre la característica naturaleza de los caracteres morfológicos y moleculares de S. andinus, pruebas que esgrimimos en apoyo de la hipótesis que esta última es una especie válida, así confirmando su escisión de S. brasiliensis. Proporcionamos detalles de los caracteres morfológicos de S. apollinaris y S. fulvescens que confirman la decisión taxonómica de asimismo separarlos de S. brasiliensis. Proporcionamos datos en aditamento que indican que a falta de cualquier material tipo para S. defilippi, este nombre es en el mejor de los casos un nomen dubium. Finalmente, ofrecemos datos y evidencia apoyando nuestras decisiones de reconocer un mayor número de especies Neotropicales de Sylvilagus que previamente se conocían.
... This procedure was necessary because the nomenclature of some species changed compared to the names used in previous trichology studies. After this procedure, we crossed the geographic distribution data of the species (IUCN, 2023), the information available in review taxonomic papers (such as for the species of the genus Sylvilagus - Silva et al., 2019) and the collection location of the hair donor specimens, to confirm the identification at a specific level. In this case, we track the collection location using the registration number of animals deposited in museums using the database of SpeciesLink (SpeciesLink, 2023). ...
The characterization of patterns of hair microstructure is an important instrument for studying the diet and ecology of mammals, representing an accessible method for identifying predators and their prey. The present study aimed to: (1) describe methodological adaptations developed to optimize traditional guard hair analysis protocols; (2) propose adjustments in the classification of morphological patterns of medulla and cuticle; and (3) establish the microstructural pattern of Brazilian mammals’ hair to assist in the identification of prey and predators in studies based on fecal samples. Hairs from 53 mammal species, including small (n = 16), medium (n = 28) and large size (n = 9), distributed in 24 families and nine orders were analyzed. The orders with the most species analyzed were Carnivora (n = 14), Rodentia (n = 13) and Didelphimorphia (n = 8), while the most representative families were Didelphidae (n = 8), Cricetidae (n = 7) and Felidae (n = 6). Among the species, 13 (24.5% of the total) did not have the microstructural patterns described in studies developed previously in Brazilian territory: Alouatta guariba, Blarinomys breviceps, Bradypus torquatus, Callicebus personatus, Callithrix geoffroyi, Dasyprocta leporina, Hylaeamys seuanezi, Potos flavus, Priodontes maximus, Rhipidomys mastacalis, Sapajus robustus, Sylvilagus minensis and Tayassu pecari. More descriptive nomenclatures were proposed regarding the observed patterns and new patterns were described for species evaluated in previous studies. Our results contribute to the diagnosis of species to be more accurate, contributing to the development of future studies.
... A su vez, teniendo en cuenta el gran número de subespecies descritas y nuevos registros a lo largo de su distribución (Dantas et al. 2016), se requiere profundizar los estudios de distribución biogeográfica y filogenéticos sobre el tapetí (Barquez et al. 2006;Silva et al. 2019). Ello implica que se deben aumentar los esfuerzos para caracterizar las distintas poblaciones de la especie, la conectividad ambiental y genética que exista entre ellas, particularmente en aquellas regiones donde la fragmentación de hábitat se haya acentuado y las poblaciones puedan encontrarse aisladas de las demás. ...
El tapetí, Sylvilagus brasiliensis, es el único representante de su género en Sudamérica. Hasta el momento solo existía un registro en Córdoba que data del 2002. Usando cámaras trampa para monitorear meso y macromamíferos en la porción sur del Gran Chaco Americano, se comprueba, mediante un muestreo sistemático, la presencia del tapetí para la provincia de Córdoba. Este registro verifica la presencia de esta especie en la porción sur de su distribución luego de 15 años sin registros. La presencia del tapetí en un contexto de hábitat fragmentado y de rápida deforestación del bosque chaqueño requiere generar urgentes políticas para su conservación.
... Cottontail rabbits of the genus Sylvilagus Gray, 1867 are highly speciose, with about 30 valid species (Ruedas et al. 2017. Sylvilagus is endemic to the Americas and is widely distributed from southeastern Canada to northern Argentina (Chapman and Ceballos 1990;Silva et al. 2019), occupying temperate, tropical, and subtropical habitats (Schai-Braun and Hackländer 2016). ...
Sylvilagus andinus (Thomas, 1897) is a highland lagomorph from the Ecuadorean Paramos. Its distribution was tentatively believed to extend to northwestern Peru on the basis of ecological niche modeling and the inclusion of the Peruvian S. capsalis Thomas, 1913 as a synonym. Here, we confirm the occurrence of S. andinus in Peru by a morphological examination of seven new records from northwestern Peru and one new record from Ancash department in central Peru.
... Igualmente, para el género Sylvilagus las poblaciones al occidente de Colombia fueron asignadas como S. sanctaemartae a pesar de que aún persiste confusión con la especie S. superciliaris, que podría distribuirse en la región norte del país (Ruedas et al., 2017Silva et al., 2019 Por su parte, es necesario incrementar la recolección de más material biológico y la revisión de especímenes de museos, al igual que la aplicación de nuevos métodos de registros, como los monitoreos acústicos y el uso de fototrampeo, que permitirían adicionar algunas especies que han sido registradas en departamentos aledaños y que presentan amplia distribución, como murciélagos de los géneros Anoura y Platyrrhinus (Granados-Peña, 2013;Racero-Casarrubia et al., 2015;Avendaño-Maldonado et al., 2021;Chacón-Pacheco et al., 2022), y esclarecer la taxonomía de aquellas con registros dudosos. Asimismo, para el presente listado la falta de exploraciones para algunas áreas en el departamento revela la necesidad de aumentar esfuerzos en áreas pobremente representadas como las subregiones Mojana, Sabanas y San Jorge (Figura 2). ...
We present a list of mammals in the department of Sucre, based on the review of specimens deposited in biological collections, new and verifiable records in scientific literature. We found 143 species, representing 26.3% of mammals recorded for Colombia. Five species are endemic to Colombia, Cebus versicolor, Pattonomys semivillosus, Proechimys chrysaeolus, Saguinus oedipus and Sylvilagus sanctaemartae; five are categorized as Data Deficient, and 13 and 17 in some category of threat at national and global level, respectively. The bat Ametrida centurio is recorded for the first time in Colombia, based on a photograph taken in the municipality of Santiago de Tolú. We recorded higher species richness to the north of the department, in the sub-regions Golfo de Morrosquillo and Montes de Maria, probably the result of the increased collection effort. It is necessary to increase local efforts, due to insufficient or null exploration in some areas of the department.
... Due to taxonomic uncertainties regarding the species of cottontails in western São Paulo, where both Sylvilagus minensis and S. paraguensis could occur, we refer to the taxon in SMA as Sylvilagus sp. (Silva et al., 2019). We consider the red brocket in the area to be Mazama rufa instead of M. americana, following Peres et al. (2021). ...
The seasonal forest formations of the Atlantic Forest are a threatened and poorly known habitat. We present here a list of the non-volant mammals occurring in a 515-ha forest fragment known as Santa Maria and located in the Brazilian state of São Paulo. Our surveys are based on live trap captures, camera traps, and active searches for footprints, as well as secondary data. We list 29 species of non-volant mammals in the fragment, recorded between 1996 and 2021. One species found in the fragment, Leontopithecus chrysopygus, is globally endangered. Two species are classified as "vulnerable" in the global red list: Myrmecophaga tridactyla, and Tapirus terresris. One species, Panthera onca, is classified as "critically endangered" in São Paulo state. The red howler, Alouatta guariba, was not recorded after 1999 and has probably been extirpated in the fragment. We show that the number of non-volant mammal species in Santa Maria fragment is high, in relation to its size. The fragment is also in a strategic position, between the Morro do Diabo state park and the Black Lion Tamarin Ecological station, the two largest protected areas in the region. Considering its high mammal richness and its possible role as stepping stone for the local fauna, we recommend that the fragment become a protected area.
... O gênero Cebus é utilizado conforme argumentado porGutiérrez & Marinho-Filho (2017). O tapiti é aqui referido como Sylvilagus sp., pois estudos recentes indicam que Sylvilagus brasiliensis (Linnaeus, 1758) representa um complexo de espécies (e.g.,Ruedas et al., 2019;Silva et al., 2019). São indicadas as espécies endêmicas do Bioma Mata Atlântica (conformeGraipel et al., 2017), ameaçadas em nível global (IUCN, 2020), nacional (MMA, 2014) e estadual (RioGrande do Sul, 2014;Santa Catarina, 2011), assim como as espécies exóticas invasoras conforme definidas pela CBD(2002)e listadas em Rio Grande do Sul (2013) e Santa Catarina (2012). ...
As florestas estacionais são ecossistemas marcados por grande sazonalidade climática, que ocorrem na região tropical em todo o mundo e estão associadas aos vários biomas brasileiros. Apesar do clima subtropical, estas florestas também ocorrem no sul do Brasil, na calha do rio Uruguai e seus principais afluentes, uma região ainda carente em estudos sobre a fauna. Neste sentido, apresentam-se aqui os resultados obtidos com o levantamento da mastofauna durante a etapa de implantação da Usina Hidrelétrica Foz do Chapecó, na divisa entre os estados de Santa Catarina e Rio Grande do Sul, no período de setembro de 2007 a junho de 2010. Foram empregados os métodos de observação direta, levantamento de vestígios e atropelamentos, armadilhas fotográficas, captura de pequenos mamíferos com armadilhas de arame e chapa de alumínio e com armadilhas de interceptação e queda, captura de morcegos com redes de neblina, busca por colônias e entrevistas. Foram registradas 68 espécies, pertencentes a 22 famílias e nove ordens de mamíferos, incluindo 16 espécies ameaçadas e duas exóticas. A riqueza de pequenos mamíferos foi relativamente alta. Akodon spp. e Oligoryzomys nigripes foram as espécies mais abundantes entre os não voadores, e Sturnira lilium e Artibeus spp. entre os morcegos. Várias espécies de médio e grande porte registradas são raras ou estão extintas localmente. Esses dados possivelmente refletem os impactos da grande perda de cobertura floresta e da pressão caça, cuja mitigação é fundamental para conservação da biota regional.
... Para a identificação taxonômica dos gêneros e espécies foram utilizadas as seguintes referências: Artiodactyla (Wilson & Reeder, 2005), exceto para Dicotyles tajacu (Acosta et al., 2020); Carnivora (Wilson & Reeder, 2005), exceto para Leopardus tigrinus (Nascimento & Feijó, 2017;Trigo et al., 2013), Herpailurus e Puma (Kitchener et al., 2017;Segura et al., 2013); Cingulata (Gardner, 2008), exceto para Cabassous (Feijó & Anacleto, 2021) e Dasypus (Feijó et al., 2018); Chiroptera (Gardner, 2008;Garbino et al., 2020); Didelphimorphia (Rossi et al., 2012), exceto para Metachirus (Voss et al., 2019), Monodelphis (Pavan & Voss, 2016) e Philander (Voss et al., 2018); Lagomorpha (Ruedas et al., 2017;Silva et al., 2019); Perissodactyla (Wilson & Reeder, 2005); Pilosa (Gardner, 2008); Primates ; e Rodentia , exceto para Abrawayaomys (Percequillo et al., 2017), Calomys mattevii (Gurgel-Filho et al., 2015), Castoria (Pardinãs et al., 2016), Hylaeamys (Brennand et al., 2013) e Oecomys (Suarez--Villota et al., 2018). Para famílias e ordens foi utilizado Burgin et al. (2018), com exceção de Artiodactyla (Prothero et al., 2021). ...
O professor João Moojen iniciou uma importante coleção de vertebrados na Escola Superior de Agricultura e Veterinária do estado de Minas Gerais, em Viçosa em 1933. Essa coleção foi o embrião do Museu de Zoologia João Moojen da Universidade Federal de Viçosa (MZUFV), inaugurado oficialmente em 1993. Atualmente, o MZUFV possui coleções científicas, didática e de exposição, com dados digitalizados de aproximadamente 36 mil exemplares, incluindo fósseis e viventes de peixes, anfíbios, répteis, aves e mamíferos. O objetivo deste estudo foi descrever o histórico da Coleção de Mamíferos do MZUFV, evidenciar sua diversidade taxonômica e abrangência geográfica. Com essa finalidade, a identidade taxonômica dos espécimes foi examinada e atualizada, e um mapa de procedência foi produzido. Foram contabilizados 4878 espécimes tombados pertencentes a 218 espécies distribuídas em 11 ordens, 35 famílias e 142 gêneros. As espécies do acervo representam 25,5 % da diversidade de mamíferos no Brasil. A maioria dos exemplares é oriundo da Mata Atlântica de Minas Gerais, havendo também representantes dos biomas Cerrado, Pantanal e Amazônia. As ordens mais representadas tanto em espécimes quanto espécies são Rodentia, Chiroptera, Didelphimorphia, Carnivora e Primates. Na coleção estão depositados parátipos dos roedores Calassomys apicalis e Rhipidomys tribei. A contratação de mastozoólogos desde a década de 1990 aumentou o número de exemplares na coleção através de projetos e parcerias nacionais e internacionais. Desde sua criação, o acervo tem sido utilizado em inúmeras publicações científicas, enfatizando sua relevância regional e nacional.
... O gênero Cebus é utilizado conforme argumentado porGutiérrez & Marinho-Filho (2017). O tapiti é aqui referido como Sylvilagus sp., pois estudos recentes indicam que Sylvilagus brasiliensis (Linnaeus, 1758) representa um complexo de espécies (e.g.,Ruedas et al., 2019;Silva et al., 2019). São indicadas as espécies endêmicas do Bioma Mata Atlântica (conformeGraipel et al., 2017), ameaçadas em nível global (IUCN, 2020), nacional (MMA, 2014) e estadual (RioGrande do Sul, 2014;Santa Catarina, 2011), assim como as espécies exóticas invasoras conforme definidas pela CBD(2002)e listadas em Rio Grande do Sul (2013) e Santa Catarina (2012). ...
As florestas estacionais são ecossistemas marcados por grande sazonalidade climática, que ocorrem na região tropical em todo o mundo e estão associadas aos vários biomas brasileiros. Apesar do clima subtropical, estas florestas também ocorrem no sul do Brasil, na calha do rio Uruguai e seus principais afluentes, uma região ainda carente em estudos sobre a fauna. Neste sentido, apresentam-se aqui os resultados obtidos com o levantamento da mastofauna durante a etapa de implantação da Usina Hidrelétrica Foz do Chapecó, na divisa entre os estados de Santa Catarina e Rio Grande do Sul, no período de setembro de 2007 a junho de 2010. Foram empregados os métodos de observação direta, levantamento de vestígios e atropelamentos, armadilhas fotográficas, captura de pequenos mamíferos com armadilhas de arame e chapa de alumínio e com armadilhas de interceptação e queda, captura de morcegos com redes de neblina, busca por colônias e entrevistas. Foram registradas 68 espécies, pertencentes a 22 famílias e nove ordens de mamíferos, incluindo 16 espécies ameaçadas e duas exóticas. A riqueza de pequenos mamíferos foi relativamente alta. Akodon spp. e Oligoryzomys nigripes foram as espécies mais abundantes entre os não voadores, e Sturnira lilium e Artibeus spp. entre os morcegos. Várias espécies de médio e grande porte registradas são raras ou estão extintas localmente. Esses dados possivelmente refletem os impactos da grande perda de cobertura floresta e da pressão caça, cuja mitigação é fundamental para conservação da biota regional.
... The geographic range of the Vulnerable Rio de Janeiro Dwarf Cottontail, Sylvilagus tapetillus, is uncertain (Quintela et al. 2020), and data on its current distribution are scarce. Some authors have suggested the possible extinction of the species due to high human population density and the degradation of natural habitats in the state of Rio de Janeiro (Ruedas et al. 2017;Silva et al. 2019). Thus, new findings such as the records of S. tapetillus in the ARIE-FC presented here, just 25 km southeast of its type locality area, are a highly important contribution to the knowledge and conservation of this species and for the confirmation of its occurrence in the middle Paraíba do Sul river region. ...
The Atlantic Forest is one of the most biodiverse biomes in the world and has been severely degraded and fragmented, with the extirpation of most medium-sized and large vertebrates from the forest remnants. Here we present the results of a survey of medium-sized and large mammals in an area of protected seasonal semideciduous forest, the Floresta da Cicuta Area of Relevant Ecological Interest (ARIE-FC), Rio de Janeiro, Brazil, part the Atlantic Forest biome. We used camera traps (2,257 camera days) and direct observations over a 23-month period. We recorded 19 species (including two domestic species), seven of which are classified as at-risk, such as Leopardus guttulus (Hensel, 1872), Sylvilagus tapetillus Thomas, 1913, Alouatta clamitans Cabrera, 1940, and Chrysocyon brachyurus (Illiger, 1815). A diverse terrestrial mammal assemblage in the ARIE-FC reinforces the importance of small forest fragments for the conservation of biodiversity in human-modified landscapes of the Brazilian Atlantic Forest.
... (cottontail rabbits)(Ruedas 2017;Silva et al 2019;Kim et al 2019), first recorded in the fossil deposits dating back about 8.6 and 7.2 million years ago, respectively. Then a diversification of their morphology, anatomy, physiology and ecology followed(Lacher et al 2016). ...
The present work aims to synthesize the origin and phylogeny of the European rabbit (Oryctolagus cuniculus), of the Family Leporidae, Order Lagomorpha. Lagomorpha is an order of mammals which splits into two living families: Family Leporidae and Family Ochotonidae. Lagomorpha may have descended from the group of mimotonids (Anagaloidea). The diversity of Lagomorphs was certainly higher in the past than in the present, with around 75 genera and more than 230 species represented in the fossil record. These statistics of fossil record are evidences supporting that lagomorph lineages are declining in the present times. The living genera of the Family Leporidae emerged in the early Miocene, with the two most diverse genera, Genus Lepus (hare species) and Genus Sylvilagus (cottontail rabbits), first recorded in the fossil deposits dating back about 8.6 and 7.2 million years ago, respectively. The literature is scarce regarding the phylogeny of Genus Oryctolagus. The genus Oryctolagus comprises a single species (O. cuniculus) and six subspecies, and is the ancestor of all domesticated breeds. The paradox of this species is that, although the group to whom it belongs is in decline, the European rabbit is a species with an extraordinary plasticity, giving birth to a multitude of breeds and varieties of shape and color.
Camera traps became the main observational method of a myriad of species over large areas. Data sets from camera traps can be used to describe the patterns and monitor the occupancy, abundance, and richness of wildlife, essential information for conservation in times of rapid climate and land‐cover changes. Habitat loss and poaching are responsible for historical population losses of mammals in the Atlantic Forest biodiversity hotspot, especially for medium to large‐sized species. Here we present a data set from camera trap surveys of medium to large‐sized native mammals (>1 kg) across the Atlantic Forest. We compiled data from 5380 ground‐level camera trap deployments in 3046 locations, from 2004 to 2020, resulting in 43,068 records of 58 species. These data add to existing data sets of mammals in the Atlantic Forest by including dates of camera operation needed for analyses dealing with imperfect detection. We also included, when available, information on important predictors of detection, namely the camera brand and model, use of bait, and obstruction of camera viewshed that can be measured from example pictures at each camera location. Besides its application in studies on the patterns and mechanisms behind occupancy, relative abundance, richness, and detection, the data set presented here can be used to study species' daily activity patterns, activity levels, and spatiotemporal interactions between species. Moreover, data can be used combined with other data sources in the multiple and expanding uses of integrated population modeling. An R script is available to view summaries of the data set. We expect that this data set will be used to advance the knowledge of mammal assemblages and to inform evidence‐based solutions for the conservation of the Atlantic Forest. The data are not copyright restricted; please cite this paper when using the data.
Human activities and biological invasions have caused unprecedented biodiversity loss over the past 500 years. Proximity to humans drives the spatial distribution of species toward less disturbed habitats. Invasive species can competitively exclude native species, but species may coexist due to different habitat preferences. Here, we investigated how proximity to farms and the presence of the non‐native European hare ( Lepus europaeus ) influence the habitat use by the Brazilian cottontail ( Sylvilagus minensis ) in southeastern Brazil. We found that the probability of cottontail site use increased with native forest cover and decreased with farmhouse proximity, ranging from 0.05 (SE = 0.02) at sites close to farmhouses (≅900 m) with no native forest to 0.70 (SE = 0.15) at sites far from farmhouses (≅2500 m) dominated by native forest. Higher risk of harassment and predation by free‐roaming dogs and cats may explain the negative effect of farmhouse proximity on cottontail habitat use. We found little evidence for competitive exclusion by the European hare. Instead, our results suggest that the two species spatially segregate due to different habitat preferences. While the European hare more likely uses farmland in its native and non‐native range, our results suggest that the Brazilian cottontail is a forest dweller. Although we found only weak evidence of competitive exclusion, we advise caution because invasive species may delay the onset of detrimental effects due to initial low population densities in newly invaded areas as is the case of the European hare in southeastern Brazil.
Abstract in Portuguese is available with online material.
The taxonomic status and interspecies relationships of hares (genus Lepus ) in Xinjiang, China, remain ambiguous owing to extremely similar external morphologies, introgressive hybridization between species and a lack of molecular genetic records. In this study, a total of 154 hare specimens were used to clarify their taxonomic status. Based on multiple lines of evidence, including observations and comparisons of external morphological characteristics, skull morphometrics and genome‐wide single nucleotide polymorphism (SNP) datasets, four hare species were recognised. Lepus yarkandensis and Lepus timidus , which have obvious morphological characteristics, were identified as two distinct species, as previously reported. Combining the integrated morphological and molecular datasets with the relevant literature, we proposed suggestions on the classification of the more controversial hares. Due to molecular and morphological similarities, hares in northern and central Xinjiang were divided into two subspecies of Lepus tolai , namely, Lepus tolai lehmanni and Lepus tolai centrasiaticus . Despite similar external morphological characters, hares in the southwest Pamir Plateau and its surroundings can be distinguished from L. tolai by differences in skull morphology and genetic divergence and were, therefore, considered a subspecies of Lepus tibetanus , Lepus tibetanus pamirensis . Furthermore, we found that hybridization and introgression occurred between sympatric or parapatric hares, especially between L. yarkandensis and L. tibetanus pamirensis , L. yarkandensis and L. tolai centrasiaticus , and L. tolai lehmanni and L. timidus .
This chapter provides an overview of the knowledge on mammals in the Campos Sulinos. To date, 134 native species have been recorded, of which eleven are endemic. Through a topical analysis of the literature produced so far, we present research priorities on several topics and subregions. Currently, there is a reasonable body of knowledge on small mammal and carnivore population genetics and habitat selection, whereas other groups and topics are still poorly studied, such as the ecology of armadillos. Most of the knowledge comes from studies conducted in the west and south of the Brazilian Pampa, while studies in the highland grasslands and in the northwest and center of the Pampa have been scarce. Hybridization, recently described species, and adaptations for living in open environments are discussed, with an emphasis on the need to conserve species and ecosystem services in the region. The future systematic planning of mammal conservation in the Campos Sulinos depends on filling knowledge gaps and developing taxonomically and spatially more comprehensive research, as well as on a better connection between researchers and decision-makers/stakeholders.
Ongoing declines in the imperiled New England cottontail Sylvilagus transitionalis have coincided with the introduction and expansion of the closely related eastern cottontail Sylvilagus floridanus. These paired population trends have led to the inference of competition between the two species. Competition between native and introduced species has often involved overlapping use of food resources, but limited effort has been spent to analyze the diets of New England cottontail and eastern cottontail and to evaluate the potential for resource competition. We used microhistological analysis of fecal pellets to assess the winter diets of both species and we compared diet composition with available plant communities to evaluate their preferences for dietary items across southern New England and southeastern New York. We found no differences in diets between New England cottontail and eastern cottontail, although diets did differ between regions within the study area. Diet preferences also were consistent between the species and largely excluded non-native plant genera. Our results demonstrate that these species are generalist herbivores and that there is high potential for competition for food resources in the winter between them, although the present lack of diet partitioning may indicate the presence of other factors limiting competition. This study highlights the need for careful evaluation of interactions between native and non-native species, a prerequisite for developing conservation plans that appropriately account for interspecific competition.
The Anthropocene brought an accelerated risk of extinction for species across the globe. However, extinction proneness is not even across groups. Past and current events show large-sized mammals at greater extinction risk than smaller ones. For practical reasons, conservation actions tend to focus on the species level; therefore, well-founded species limits are pivotal. Since 2005, the number of known mammal species is about 20% higher but largely due to taxonomic discoveries in small-sized taxa. Here we review the recent taxonomic advances on medium- and large-sized mammals (MLM) from the Neotropics, and discuss misperceptions concerning the taxonomy stability in this group and how this may hinder proper conservation actions. We advocate that apparent taxonomic inertia toward large-sized mammals is partly related to limited systematic inquiry rather than representing an accurate knowledge of their diversity. Fortunately, this scenario has slowly changed in recent years. Linked to integrative analyses that took place during the 21st century, the Neotropical region represents a major example of recent growth in MLM diversity. Taxonomic novelties were found in eight orders of MLM and occurred across taxonomic ranks, from family to subspecies. Most changes comprise subspecies or synonyms elevated to full species, but new taxa of Artiodactyla, Carnivora, Lagomorpha, Pilosa, Primates, Perissodactyla, and large rodents have also been discovered. Recent reshuffles in MLM classification clearly illustrate the risk that bias in taxonomy studies can bring to conservation. Considering the new findings, some species previously labeled as “least concern” for conservation, stand now in some level of threat. This appraisal challenges the misperception of MLM as well-known and shows that taxonomy is a conservation issue.
An updated and annotated checklist of mammals occurring in Brazil is presented. A total of 751 native species, distributed in 249 genera, 51 families and 11 orders were recorded to the country. The Brazilian mammalian fauna shows an elevated rate of endemism (30%; 223 species). Among the species evaluated by IUCN (668 species; 90%), a total of 80 (10.6% of total mammalian fauna) are Threatened, 28 (3.9%) are considered as Near Threatened, two species (0.3%) are presumable Extinct, 96 (12.8%) are considered with Defi cient Data for conservation and 462 (61.6%) are considered as Least Concern. Fifteen new species were described since the last national compilation (published in 2017), which associated to new records to the country and synonimizations resulted in an increment of 30 species. Eight non-native species were introduced to the country, including the recently established Asiatic cervids Rusa unicolor (sambar) and Axis axis (chital). Seven native species (fi ve primates and two hystricomorph rodents) have been translocated from their areas of natural occurrence to other areas inside the country.
Evolution of Lagomorphs luis a. ruedas, josé m. mora, and hayley c. lanier What, if anything, is a rabbit? (Wood 1957:417) As currently understood, the order Lagomorpha has two living families: the Ochotonidae (pikas) and the Leporidae (cottontails and hares or jackrabbits). There are 29 extant species of pika in the genus Ochotona, whereas the Leporidae includes 63 species in 11 genera. The Sardinian pika, †Prolagus sardus, represents a third, recently extinct family of pika relatives, the †Prolagidae. However, and notwithstanding this apparent simplicity, both the taxonomic and the evolutionary histories of the Lagomorpha are complex and have been extensively debated. The original taxonomic understanding of the Lagomorpha (Linnaeus 1758) was unusual by modern standards. Linnaeus recognized eight orders of mammals, ranging taxonomically from what we might today consider a family (the whales, “Cetae”) to strange collections of subclasses (his “Bestiæ” and “Glires”). Lagomorphs were in the order Glires, which included six genera: Rhinoceros (rhinoceroses, two species), Hystrix (porcupines, five species), Lepus (hares and cottontails, four species), Castor (beaver, two species), Mus (mice and allies, 15 species), and Sciurus (squirrels, seven species). Thus the first taxonomic association of Lagomorpha was in what we might today consider a group of several distinct orders including rodents and, incongruously, an odd- toed ungulate: the rhinoceros. Linnaeus’s “genera” in Glires are in fact akin to modern families, if not orders. Linnaeus did not include pikas in the definitive tenth edition of his nomenclatural treatise; the four species included in Lepus were L. timidus, L. capensis, “Lepus” (= Oryctolagus) cuniculus, and “Lepus” (= Sylvilagus) brasiliensis. As a bit of trivia, the legendary modern “jackalope” appears to have been known to Linnaeus, who noted (1758:57) that the horned hare, if not a hybrid, was almost certainly mythical. In the particular instance of Lepus in the tenth edition, Linnaeus’s family concept was identical to what today we would call Leporidae. However, his diagnosis of the genus Lepus based on the duplicated first pair of upper incisors is in fact the modern diagnosis of the order Lagomorpha (Gidley 1912). Illiger (1811) used that character to erect the family Duplicidentata (still within the rodents), including two genera: Lepus and Lagomys (= Ochotona). Fischer called this same family- level group of Lepus and Lagomys the Leporini (Fischer 1817:372) and Leporinorum (Fischer 1817:409). The first use of “Leporidae” was by Gray (1821:304); however, he used the term in the same sense as Illiger and Fischer, to include Lepus and Lagomys (thus corresponding to Lagomorpha) in his order Rosores. Waterhouse (1839) later split “rodents” into three higher categories, or sections, the third of which, Leporina, corresponded to the contemporary concept of Lagomorpha. It was Brandt (1855:295) who eventually coined for the group the now commonly used term “Lagomorpha” (“hare shaped”), also at the subordinal rank within rodents (along with Sciuromorpha, Myomorpha, and Hystricomorpha). In addition, although he clearly called lagomorphs a suborder (“Subordo IV. Lagomorphi seu 1709048_int_cc2015.indd 4 15/9/2017 15:59 Evolution of Lagomorph 5 Lagomorpha”), Brandt (1855:295) began his discussion of the groups with the words “Ordo Leporinus.,” underscoring their stark distinction from rodents, based on the presence of four upper incisors in lagomorphs. Thus, while it could be argued that Brandt was the first to suggest ordinal status for lagomorphs, it was not until 1912 that J. W. Gidley formally called for ordinal rank for the Lagomorpha. Evolutionary History and Chronology of the Lagomorpha—Interordinal Relationships The early evolutionary diversification of Glires, the group including both rodents and lagomorphs, has been hypothesized to have occurred in the Late Cretaceous, immediately preceding the Cretaceous- Paleogene boundary (Asher et al. 2005), some 66 mya (near the time that non- avian dinosaurs went extinct). Evidence for this early diversification comes from the extinct †Mimotonidae, a non- natural grouping (in this instance, not including all descendants from a last common ancestor) of Glires forming with Lagomorpha the Duplicidentata, and the acknowledged closest relatives to Lagomorpha (Asher et al. 2005). Successive sister groups included †Gomphos elkema and also the non- natural †Eurymylidae (Asher et al. 2005). Within Lagomorpha, as currently understood, the earliest known fossil dates to at least 53 mya and is known from Early Eocene Cambay Shale deposits in west- central India from the Vastan lignite mine (Rose et al. 2008). Prior to that report, the oldest Lagomorpha were dated to the Irdinmanhan (48.6–37.2 mya; Middle Eocene) of Asia.
Accurate taxonomy is central to the study of biological diversity, as it provides the needed evolutionary framework for taxon sampling and interpreting results. While the number of recognized species in the class Mammalia has increased through time, tabulation of those increases has relied on the sporadic release of revisionary compendia like the Mammal Species of the World (MSW) series. Here, we present the Mammal Diversity Database (MDD), a digital, publically accessible, and updateable list of all mammalian species, now available online: https://mammaldiversity.org. The MDD will continue to be updated as manuscripts describing new species and higher taxonomic changes are released. Starting from the baseline of the 3rd edition of MSW (MSW3), we performed a review of taxonomic changes published since 2004 and digitally linked species names to their original descriptions and subsequent revisionary articles in an interactive, hierarchical database. We found 6,495 species of currently recognized mammals (96 recently extinct, 6,399 extant), compared to 5,416 in MSW3 (75 extinct, 5,341 extant)—an increase of 1,079 species in about 13 years, including 11 species newly described as having gone extinct in the last 500 years. We tabulate 1,251 new species recognitions, at least 172 unions, and multiple major, higher-level changes, including an additional 88 genera (1,314 now, compared to 1,226 in MSW3) and 14 newly recognized families (167 compared to 153). Analyses of the description of new species through time and across biogeographic regions show a long-term global rate of ~25 species recognized per year, with the Neotropics as the overall most species-dense biogeographic region for mammals, followed closely by the Afrotropics. The MDD provides the mammalogical community with an updateable online database of taxonomic changes, joining digital efforts already established for amphibians (AmphibiaWeb, AMNH’s Amphibian Species of the World), birds (e.g., Avibase, IOC World Bird List, HBW Alive), non-avian reptiles (The Reptile Database), and sh (e.g., FishBase, Catalog of Fishes).
Using 26 cranial measurements, we conducted a morphometric study on 113 adult skulls of the currently recognized rabbits Sylvilagus brasiliensis and S. sanctaemartae from Colombia, Ecuador, and Peru. Five morphological groups are identified of which 4 warrant species-level recognition. North and west of the Andes, S. gabbi occupies the lowlands of northern Colombia and northwestern Ecuador. Sylvilagus sanctaemartae is morphologically indistinguishable from S. gabbi and is a synonym of it. Two species live in the Andes of Colombia: S. fulvescens in the Western and Central Andes and S. apollinaris in the Eastern Andes. East of the Andes, Sylvilagus brasiliensis defilippi is found in the tropical Orinoco and Amazon basins of Colombia, Ecuador, and Peru, and S. brasiliensis andinus occurs in the Andes of Ecuador. These 2 subspecies intergrade in the Amotape-Huancabamba Zone of extreme southern Ecuador and adjacent west-central Peru. The eastern distributional limit of S. b. defilippi outside the study area in South America is unknown. An additional 50 skulls of S. gabbi and 14 of S. dicei were examined from Costa Rica and Panama to compare with the rabbits from South America. The data show that S. gabbi exhibits no noticeable geographic variation from Central America to northern Colombia and northwestern Ecuador. Sylvilagus dicei from the Cordillera de Talamanca of Costa Rica and Panama is morphologically most similar to S. fulvescens from the Western and Central Andes of Colombia and they are likely closely related. Methods are presented to identify all taxa and the distribution of each taxon is provided. This taxonomic arrangement is based on few specimens. Accordingly, species boundaries and phylogenetic relationships should be tested by focusing future collecting and morphological and molecular research in high-priority areas such as: 1) along the Colombian-Ecuadorian border from the Pacific Coast, across the Andes into the Amazon Basin; 2) Amotape-Huancabamba Zone of Ecuador and Peru; and 3) Eastern Andes of Colombia.
Of the 19 currently recognized species of Sylvilagus Gray, 1867, 15 inhabit North America, and only 5 are recognized
in South America: S. brasiliensis Linnaeus, 1758 (throughout most of the continent); S. varynaensis Durant and
Guevara, 2001, restricted to the southern lowlands of Venezuela (states of Barinas, Portuguesa, and Guarico);
S. andinus (Thomas, 1897) from the Andean páramos of Ecuador and potentially in a sporadic manner to the
Colombian and Venezuelan páramos; and S. tapetillus Thomas, 1913, from the coastal plain in the region of Rio de
Janeiro. In addition to these, putative subspecies of S. floridanus, primarily a North American taxon, nominally are
recognized from the grassland plains areas of northwestern South America east of the Andes. While S. varynaensis
and S. tapetillus are monotypic, S. brasiliensis contains at least 37 named taxa in synonymy, distributed in various
habitats; S. andinus requires further study. As a result of the recent description of a neotype for S. brasiliensis,
it is now possible to assess species limits and begin the process of illuminating formerly obscured biological
diversity in South American cottontails. Here, I describe a new species of Sylvilagus from the lowlands of western
Suriname, and excise S. sanctaemartae Hershkovitz, 1950 from synonymy with S. brasiliensis.
We assess progress toward the protection of 50% of the terrestrial biosphere to address the species-extinction crisis and conserve a global ecological heritage for future generations. Using a map of Earth's 846 terrestrial ecoregions, we show that 98 ecoregions (12%) exceed Half Protected; 313 ecoregions (37%) fall short of Half Protected but have sufficient unaltered habitat remaining to reach the target; and 207 ecoregions (24%) are in peril, where an average of only 4% of natural habitat remains. We propose a Global Deal for Nature—a companion to the Paris Climate Deal—to promote increased habitat protection and restoration, national-and ecoregion-scale conservation strategies, and the empowerment of indigenous peoples to protect their sovereign lands. The goal of such an accord would be to protect half the terrestrial realm by 2050 to halt the extinction crisis while sustaining human livelihoods.
The current distribution and genetic relationships among populations of jackrabbits of the genus Lepus in the Baja California Peninsula and adjacent islands resulted from climate warming and rising sea levels following the Last Glacial Maximum, ~21 000 years BP. The colour pattern of the pelage and the genetic, biogeographic, and taxonomic relationships among peninsular and insular jackrabbit populations were investigated using four mitochondrial DNA genes (Cyt b, DLoop, COI, and COIII) and one nuclear gene (β-fib I7). The phylogenetic analyses identified two clades, one of them with three well-supported subclades that corresponded to three geographical groups within the Baja California Peninsula (including insular populations), with a slight genetic differentiation between these subclades (average of 0.5%). The second clade corresponded to a group outside the Baja California Peninsula. Insular populations appear to have been isolated within the last 5000 years. We recommend dividing L. californicus in the Baja California Peninsula and adjacent islands into four groups at subspecific level.
Birds have arguably been the most intensely studied animal group for their phylogenetic relationships. However, the recent advent of genome-scale phylogenomics has made the forest of bird phylogenies even more complex and confusing. Here, in this perspective piece, I show that most parts of the avian Tree of Life are now firmly established as reproducible phylogenetic hypotheses. This is to the exception of the deepest relationships among Neoaves. Using phylogenetic networks and simulations, I argue that the very onset of the super-rapid neoavian radiation is irresolvable because of eight near-simultaneous speciation events. Such a hard polytomy of nine taxa translates into 2 027 025 possible rooted bifurcating trees. Accordingly, recent genome-scale phylogenies show extremely complex conflicts in this (and only this) part of the avian Tree of Life. I predict that the upcoming years of avian phylogenomics will witness many more, highly conflicting tree topologies regarding the early neoavian polytomy. I further caution against bootstrapping in the era of genomics and suggest to instead use reproducibility (e.g. independent methods or data types) as support for phylogenetic hypotheses. The early neoavian polytomy coincides with the Cretaceous–Paleogene (K-Pg) mass extinction and is, to my knowledge, the first empirical example of a hard polytomy. © 2016 The Authors. Zoologica Scripta published by John Wiley & Sons Ltd on behalf of Royal Swedish Academy of Sciences.
Resumen
Los lineamientos para el uso de especies de mamíferos de vida silvestre en la investigación con base en Sikes et al. (2011) se actualizaron. Dichos lineamientos cubren técnicas y regulaciones profesionales actuales que involucran el uso de mamíferos en la investigación y enseñanza; también incorporan recursos nuevos, resúmenes de procedimientos y requisitos para reportes. Se incluyen detalles acerca de captura, marcaje, manutención en cautiverio y eutanasia de mamíferos de vida silvestre. Se recomienda que los comités institucionales de uso y cuidado animal (cifras en inglés: IACUCs), las agencias reguladoras y los investigadores se adhieran a dichos lineamientos como fuente base de protocolos que involucren mamíferos de vida silvestre, ya sea investigaciones de campo o en cautiverio. Dichos lineamientos fueron preparados y aprobados por la ASM, en consulta con profesionales veterinarios experimentados en investigaciones de vida silvestre y IACUCS, de quienes cuya experiencia colectiva provee un entendimiento amplio y exhaustivo de la biología de mamíferos no-domesticados. La presente versión de los lineamientos y modificaciones posteriores están disponibles en línea en la página web de la ASM, bajo Cuidado Animal y Comité de Uso: (http://mammalogy.org/uploads/committee_files/CurrentGuidelines.pdf). Recursos adicionales relacionados con el uso de animales de vida silvestre para la investigación se encuentran disponibles en (http://www.mammalsociety.org/committees/animal-care-and-use#tab3).
We document the first record of Sylvilagus brasiliensis (Linnaeus, 1758) in Rio Grande do Norte state, Brazil. An adult individual was photographed in October 2015 in the municipality of João Câmara. This is the northernmost report of this species for the Caatinga biome. This article also represents important data for the Rio Grande do Norte, since the mammal diversity of this state is practically unknown.
Aim To use the method of parsimony analysis of endemism to identify areas of endemism for passerine birds in the Atlantic Forest, South America, and to compare the locations of these areas with areas previously identified for birds as well as other taxa. Location The Atlantic Forest, eastern South America. Methods We analysed a matrix composed of the presence (1) or absence (0) of 140 endemic species in 24 quadrats of 1 x 1 degree distributed along the Atlantic Forest to find the most parsimonious area cladogram. Results Fourteen most parsimonious cladograms were found and then summarized in a single consensus tree. Four areas of endemism were identified: Pernambuco, Central Bahia, Coastal Bahia, and Serra do Mar. Main conclusions Avian areas of endemism in the Atlantic Forest have significant generality, as they are highly nonrandom and congruent with those of other groups of organisms. A first hypothesis about the historical relationships among the four areas of avian endemism in the Atlantic Forest is delineated. There is a basal dichotomy among areas of endemism in the Atlantic Forest, with Pernambuco forming a northern cluster and Coastal Bahia, Central Bahia and Serra do Mar comprising a southern cluster. Within the southern cluster, Central Bahia and Serra do Mar are more closely related to each other than to Coastal Bahia.
Biological invasions are difficult to control when invader’s populations attain high densities; therefore early detection is important for implementing management strategies. This study presents the first record of the European rabbit, Oryctolagus cuniculus Linneaus, 1758, in Nahuel Huapi National Park, Patagonia, Argentina and confirms its dispersion in habitats adjacent to the Siete Lagos route. Considering the potential ecological consequences of rabbit in a protected area, the early detection of this invasive species will allow the National Park Administration to implement urgent control measures in order to stop the advance.
Although phylogenetic affinities of Mexican jackrabbits within the genus Lepus have been evaluated for a few species, no study has included all 5 species occurring in Mexico. In this study we assess the phylogenetic position of the Mexican species relative to other forms within the genus and evaluate evolutionary affinities among the Mexican forms. To do so, we analyzed 57 complete cytochrome b sequences belonging to the 5 Mexican jackrabbits and 18 species of Lepus distributed across Asia, Africa, Europe and America. We performed phylogenetic tree reconstruction with the neighbor-joining, maximum parsimony and maximum likelihood approaches. We also used a minimum spanning network to evaluate relationships among Mexican species. We found 5 main phylogenetic groups within Lepus, 4 of which corresponded to geographically well defined lineages. One group included L. americanus, 3 others corresponded to Mexican, African and European species, respectively. A fifth group included Asiatic, European and American forms. Our results suggest that Mexican species constitute a monophyletic entity that evolved independently of the other American species of Lepus. Within the Mexican forms, 2 main clades are apparent; 1 that includes L. alleni, L. callotis, and L.flavigularis, previously referred to as the white-sided jackrabbits, and a second one that groups together L. californicus and L. insularis, although L. californicus is a paraphyletic relative of L. insularis.
The intergeneric phylogeny of Lagomorpha had been controversial for a long time before a robust phylogeny was reconstructed based on seven nuclear and mitochondrial DNA sequences. However, skull morphology of several endemic genera remained poorly understood. The morphology of supraorbital processes in Lagomorpha is normally used as a diagnostic characteristic in taxonomy, but whether shape change of this structure parallels its genetic divergence has not been investigated. In this study, we conducted a comparative analysis of the skull morphology of all 12 extant genera using geometric morphometrics. These results indicated that no significant phylogenetic signal is observed in the shape change of the dorsal and ventral views of the cranium as well as in the lateral view of the mandible. The supraorbital processes also show insignificant phylogenetic signal in shape change. Similarly, mapping the centroid size (averaged by genus)
of these datasets onto the phylogeny also showed insignificant phylogenetic signal. Aside from homoplasy caused by convergent evolution of skull shape, the massive extinction of lagomorphs after the late Miocene is proposed as one of the main causes for diluting phylogenetic signals in their morphological evolution. Acknowledging the loss of phylogenetic signals in skull shape and supraorbital processes of extant genera sheds new light on the long-standing difficulties for understanding higher-level systematics in Lagomorpha.
The diversification of neoavian birds is one of the most rapid adaptive radiations of extant organisms. Recent whole-genome sequence analyses have much improved the resolution of the neoavian radiation and suggest concurrence with the Cretaceous-Paleogene (K-Pg) boundary, yet the causes of the remaining genome-level irresolvabilities appear unclear. Here we show that genome-level analyses of 2,118 retrotransposon presence/absence markers converge at a largely consistent Neoaves phylogeny and detect a highly differential temporal prevalence of incomplete lineage sorting (ILS), i.e., the persistence of ancestral genetic variation as polymorphisms during speciation events. We found that ILS-derived incongruences are spread over the genome and involve 35% and 34% of the analyzed loci on the autosomes and the Z chromosome, respectively. Surprisingly, Neoaves diversification comprises three adaptive radiations, an initial near-K-Pg super-radiation with highly discordant phylogenetic signals from near-simultaneous speciation events, followed by two post-K-Pg radiations of core landbirds and core waterbirds with much less pronounced ILS. We provide evidence that, given the extreme level of up to 100% ILS per branch in super-radiations, particularly rapid speciation events may neither resemble a fully bifurcating tree nor are they resolvable as such. As a consequence, their complex demographic history is more accurately represented as local networks within a species tree.
Plio-Pleistocene climate oscillations in the different regions of Western Europe substantially influenced the evolutionary history of European leporids. Distinguishing rabbits (Oryctolagus) from hares (Lepus) in the archeological and palaeontological record of Pleistocene Europe is complicated due to the variability of their size and morphology. Here, we present the first description of two Pleistocene leporid species from Bois-de-Riquet (Lézignan-la-Cèbe, Hérault) in southern France. The first, Oryctolagus cf. giberti, exhibits similar characteristics to rabbit species documented in Spain and, thus, for the first time is recorded outside the Iberian Peninsula. The second leporid is a hare represented by very limited number of non-diagnostic remains, which, unfortunately, precludes an exact species identification. Already known from Lower Pleistocene deposits in Central Europe and Spain, the presence of Lepus sp. in southern France sheds new light on the geographic extension of these species. In this respect, Bois-de-Riquet is an important paleontological site that can further our understanding of the evolutionary history and expansion of European leporids.
A multivariate morphological analysis of 26 cranial, mandibular, and dental characters was carried out on five taxa of cottontails: Sylvilagus floridanus chapmani (J. A. Allen, 1899), S.f. cognatus (Nelson, 1907), S. f. holzneri (Mearns, 1896), S. f. robustus (Bailey, 1905), and S. nuttallii pinetis (J. A. Allen, 1894). Discrete characters of upper P2 and P3 and lower p3 were examined in the above taxa, S. n. grangerii (J. A. Allen, 1895), and S. a. audubonii in the context of cladistic analyses. In the latter series of analyses, particular attention was paid to inter- and intrapopulational variation in the S. f. floridanus (J. A. Allen, 1890) and robustus taxa and in S. audubonii (Baird, 1857). I describe dental variation among holotypes and topotypes of these three taxa. My principal objective was to assess whether or not S. robustus was a subspecies of S. floridanus. An analysis of variance indicated that robustus differed from other taxa in six characters (greatest length of skull, condylobasal length, breadth of rostrum, interbasioccipital length, width of tympanic bullae, and mastoid breadth). Principal component analysis indicated ontogenetic differences between robustus and remaining taxa. Neighbor joining analysis in every case correctly classified each specimen examined to its predetermined taxon. Besides a large difference in size, several discrete differences in cranial and dental morphology separated S. robustus from the parapatric S. f. chapmani and from the nominal subspecies, S. f. floridanus;, characters based on premolar enamel pattern in particular differentiated between S. f. floridanus and robustus. In phylogenetic analyses of 24 dental characters, S. cognatus, S. robustus, and S. holzneri were successive sister taxa to an unresolved clade consisting of two paraphyletic S. nuttallii “subspecies” and two subspecies of S. floridanus (sensu stricto). I propose that Sylvilagus robustus is a species distinct from S. floridanus and its subspecies, some of which probably also constitute distinct species. These results help clarify biogeographic problems inherent in the genus Sylvilagus under the current taxonomic framework.
A quarter of all lagomorphs (pikas, rabbits, hares and jackrabbits) are threatened with extinction, including several genera that contain only one species. The number of species in a genus correlates with extinction risk in lagomorphs, but not in other mammal groups, and this is concerning because the non-random extinction of small clades disproportionately threatens genetic diversity and phylogenetic history. Here, we use phylogenetic analyses to explore the properties of the lagomorph phylogeny and test if variation in evolution, biogeography and ecology between taxa explains current patterns of diversity and extinction risk. Threat status was not related to body size (and, by inference, its biological correlates), and there was no phylogenetic signal in extinction risk. We show that the lagomorph phylogeny has a similar clade-size distribution to other mammals, and found that genus size was unrelated to present climate, topography, or geographic range size. Extinction risk was greater in areas of higher human population density and negatively correlated with anthropogenically modified habitat. Consistent with this, habitat generalists were less likely to be threatened. Our models did not predict threat status accurately for taxa that experience region-specific threats. We suggest that pressure from human populations is so severe and widespread that it overrides ecological, biological, and geographic variation in extant lagomorphs.
Rabbit hemorrhagic disease virus (RHDV) is a highly lethal Lagovirus, family Caliciviridae, that threatens European rabbits (Oryctolagus cuniculus). Although a related virus severely affects hares, cross-species infection was only recently described for new variant RHDV2 in Cape hares (Lepus capensis). We sequenced two strains from dead Iberian hares (Lepus granatensis) collected in the 1990s in Portugal. Clinical signs were compatible with a Lagovirus infection. Phylogenetic analysis of the complete capsid gene positioned them in the RHDV genogroup that circulated on the Iberian Peninsula at that time. This is the earliest evidence of RHDV affecting a species other than European rabbits.
Mitochondria play a fundamental role in cellular metabolism, being responsible for most of the energy production of the cell in the oxidative phosphorylation (OXPHOS) pathway. Mitochondrial DNA (mtDNA) encodes for key components of this process but its direct role in adaptation remains far from understood. Hares (Lepus spp.) are privileged models to study the impact of natural selection on mitogenomic evolution because i) species are adapted to contrasting environments, including arctic, with different metabolic pressures, and ii) mtDNA introgression from arctic into temperate species is widespread. Here, we analyzed the sequences of 11 complete mitogenomes (10 newly obtained) of hares of temperate and arctic origins (including two of arctic origin introgressed into temperate species). The analysis of patterns of codon substitutions along the reconstructed phylogeny showed evidence for positive selection in several codons in genes of the OXPHOS complexes, most notably affecting the arctic lineage. However, using theoretical models, no predictable effect of these differences was found on the structure and physicochemical properties of the encoded proteins, suggesting that the focus of selection may lie on complex interactions with nuclear encoded peptides or on amino acid composition. Also, a cloverleaf structure was detected in the control region only from the arctic mtDNA lineage, which may influence mtDNA replication and transcription. These results suggest that adaptation impacted the evolution of hare mtDNA and may have influenced the occurrence and consequences of the many reported cases of massive mtDNA introgression. However the origin of adaptation remains elusive.
Abstract Accurate species delimitation in Lepus was often hindered by highly conserved morphology and frequent introgression. In this study, we used rigorous molecular species delimitation methods to evaluate the taxonomic status of Hainan hare (Lepus hainanus) which has been traditionally identified as a distinct species, or a subspecies of Burmese hare (L. peguensis). The genetic distance and phylogenetic network support L. hainanus and L. peguensis are conspecific. However, the phylogenetic species concept and Bayesian species delimitation analysis based on combined mtDNA supported they are different species. The discordance between different methods can be explained by different species criterion. By taking into account our conflict results, we hold the opinion that adoption of the phylogenetic species concept and Bayesian species delimitation analysis would increase the risk of taxonomic inflation of island biota or otherwise spatially isolated population. Conservatively, we suggest that L. hainanus and L. peguensis are conspecific based on the results of our genetic divergence and phylogenetic network exclusively.
Phylogenies are increasingly used in all fields of medical and biological research. Moreover, because of the next generation sequencing revolution, datasets used for conducting phylogenetic analyses grow at an unprecedented pace. RAxML (Randomized Axelerated Maximum Likelihood) is a popular program for phylogenetic analyses of large datasets under maximum likelihood. Since the last RAxML paper in 2006, it has been continuously maintained and extended to accommodate the increasingly growing input datasets and to serve the needs of the user community.
I present some of the most notable new features and extensions of RAxML, such as, a substantial extension of substitution models and supported data types, the introduction of SSE3, AVX, and AVX2 vector intrinsics, techniques for reducing the memory requirements of the code and a plethora of operations for conducting post-analyses on sets of trees. In addition, an up-to-date, 50 page user manual covering all new RAxML options is available.
The code is available under GNU GPL at https://github.com/stamatak/standard-RAxML.
Alexandros.Stamatakis@h-its.org.
1. Although Lagomorpha (rabbits, hares and pikas) have a long evolutionary history in Eurasia and Africa, including primitive genera of Eurasia historically considered assignable at the family level to Leporidae, the predecessors of modern rabbits were absent throughout this vast region for most of the Miocene until late in that epoch. During the early and middle Miocene, crown group Leporidae differentiated in North America, then dispersed to northern Asia in the late Miocene around 8 Ma (million years before present) and afterward. They then spread widely and apparently rapidly throughout Eurasia, reaching South Asia by 7.4 Ma and penetrating Africa about 7 Ma.
2. The apparently abrupt introduction of Leporidae is a striking late Miocene event that we call the Leporid Datum. Perceived in terms of biochrons, the Leporid Datum includes localities in Europe and western Asia of late MN11 (Mammifères Néogènes system) age and younger, and precedes by less than one million years the Bahean-Baodean land mammal age boundary in China.
3. The late Miocene spread of Leporidae throughout Eurasia was a successful invasion in terms of the numerous occurrences and abundant fossils preserved. Where dating is sufficiently robust, the Leporid Datum is late Miocene, nowhere certainly more than ∼8 Ma.
5. In contrast to this sudden and widespread invasion, rare older finds suggest two possible refinements to this scenario: stem lagomorphs close to modern Leporidae may have lingered into the middle Miocene of Eurasia, or an independent, unsuccessful leporid invasion from North America may have preceded the 8 Ma datum.
5. The Leporid Datum marks an important palaeoecological event for the Old World and complements the significance of molecular dates for origins of modern genera.
Here we introduce a general class of multiple calibration birth-death tree
priors for use in Bayesian phylogenetic inference. All tree priors in this
class separate ancestral node heights into a set of "calibrated nodes" and
"uncalibrated nodes" such that the marginal distribution of the calibrated
nodes is user-specified whereas the density ratio of the birth-death prior is
retained for trees with equal values for the calibrated nodes. We describe two
formulations, one in which the calibration information informs the prior on
ranked tree topologies, through the (conditional) prior, and the other which
factorizes the prior on divergence times and ranked topologies, thus allowing
uniform, or any arbitrary prior distribution on ranked topologies. While the
first of these formulations has some attractive properties the algorithm we
present for computing its prior density is computationally intensive. On the
other hand, the second formulation is always computationally efficient. We
demonstrate the utility of the new class of multiple-calibration tree priors
using both small simulations and a real-world analysis and compare the results
to existing schemes. The two new calibrated tree priors described in this paper
offer greater flexibility and control of prior specification in calibrated
time-tree inference and divergence time dating, and will remove the need for
indirect approaches to the assessment of the combined effect of calibration
densities and tree process priors in Bayesian phylogenetic inference.
The Davis Mountains cottontail, Sylvilagus robustus, is an endemic species of the Trans-Pecos area
of Texas. Although S. robustus previously was believed to be extirpated from the Chisos Mountains, we
confirmed existence of a population. We examined intrapopulation and interpopulation variation in S.
robustus, as well as the genetic relationship to the eastern cottontail (S. floridanus) using partial sequences of
the mitochondrial cytochrome b and control region genes. Six morphometric traits relating to overall size and
six cranial characters considered diagnostic for the two subspecies were used to confirm identification of
specimens. Our morphological analysis suggested that specimens from the Chisos and Davis Mountains were S. robustus; however, low levels of genetic divergence between S. robustus and S. floridanus appeared inconsistent with species-level recognition for S. robustus.
Jackrabbits and hares, members of the genusLepus,comprise over half of the species within the family Leporidae (Lagomorpha). Despite their ecological importance, potential economic impact, and worldwide distribution, the evolution of hares and jackrabbits has been poorly studied. We provide an initial phylogenetic framework for jackrabbits and hares so that explicit hypotheses about their evolution can be developed and tested. To this end, we have collected DNA sequence data from a 702-bp region of the mitochondrial cytochromebgene and reconstructed the evolutionary history (via parsimony, neighbor joining, and maximum likelihood) of 11 species ofLepus,focusing on North American taxa. Due to problems of saturation, induced by multiple substitutions, at synonymous coding positions between the ingroup taxa and the outgroups (OryctolagusandSylvilagus), both rooted and unrooted trees were examined. Variation in tree topologies generated by different reconstruction methods was observed in analyses including the outgroups, but not in the analyses of unrooted ingroup networks. Apparently, substitutional saturation hindered the analyses when outgroups were considered. The trees based on the cytochromebdata indicate that the taxonomic status of some species needs to be reassessed and that species ofLepuswithin North America do not form a monophyletic entity.
The cottontail rabbit species, Sylvilagus brasiliensis, is currently understood to be constituted by 18 subspecies ranging from east central Mexico to northern Argentina, and from sea level to at least 4800 m in altitude. This hypothesis of a single widespread polytypic species remains to be critically tested. In other species groups of Sylvilagus from other geographic areas, the use of chromosomal information has been important in delineating taxonomic boundaries. To date, however, no chromosomal data are available for Sylvilagus south of Mexico. Here we report the chromosomal complement of two individuals (a male and a female) putatively ascribed to Sylvilagus brasiliensis on the basis of morphological characters and collected from southern Peninsula del Azuero in Panama. The diploid number (2n) of these two individuals was 38 and the fundamental number (autosomal arms, aFN) was 72. Karyotypes of S. brasiliensis from southern Mexico have reported two chromosomal forms: 2n=36, FN=68 and 2n=40, FN=76. We complement the chromosomal data with a morphological examination of the Panama specimens and of holotype materials pertinent to the taxonomic identity of Meso-american taxa of Sylvilagus. These findings, in association with others regarding the phylogenetic relationships of Sylvilagus from the Neotropics, reinforce the idea that the current taxonomic treatment of the species merits critical scrutiny. In particular, we excise Sylvilagus gabbi from subspecific synonymy with S. brasiliensis and remove the subspecies truei from brasiliensis to grabbi.
Mimotonids have recently been recognized as the likely ancestors to Lagomorpha (rabbits, hares, and pikas). Here a new species of mimotonid, Gomphos ellae, from Tsagaan Khutel locality, Valley of Lakes, Mongolia is described. This new material shows typical mimotonid features while also exhibiting important derived lagomorph features and helps to bridge the morphological and temporal gap between mimotonids and lagomorphs. The fossils comprise a right dentary, including cheek teeth and incisor, and a partial maxilla with two teeth. The dental features of G. ellae are similar to the mimotonid G. elkema, but G. ellae is distinguished from G. elkema and all other mimotonids by its long diastema. The diastema length of G. ellae is intermediate between all other mimotonids and all living and extinct lagomorphs. This feature distinguishes mimotonids from lagomorphs and the intermediate diastemal length of G. ellae further supports a strong pattern of lengthening of the diastema throughout Duplicidentata. Geologic and paleontological evidence suggest that the specimen is of Middle Eocene age, consistent with the notion that this taxon is an advanced mimotonid that likely lies near the ancestry of the lagomorphs.
We compared the variation in mitochondrial DNA among species of cottontail rabbits in the northeastern United States to (i) assess the effects of historic transplants of eastern cottontails (Sylvilagus floridanus) on subspecific status, (ii) examine the extent of hybridization between invading eastern cottontails and declining populations of endemic New England cottontails (S. transitionalis), and (iii) evaluate the recent reclassification of S. transitionalis into two sister-species, New England cottontail and Appalachian cottontail (S. obscurus). Sequence variation in the tRNAPro and the first 310 base pairs of the control region supported a separation of the two species S. floridanus and S. transitionalis/S. obscurus. However, geographic structuring of haplotypes was not detected for either group. Genetic similarity among populations of S. floridanus indicated that subspecific designations are not warranted for this species in the northeastern United States. Comparisons of sequence information from populations of S. transitionalis/S. obscurus that were never sympatric (Maine), recently sympatric (New Hampshire), or sympatric with eastern cottontails since the last glaciation of eastern North America (Virginia, West Virginia, Maryland, North Carolina) indicated that hybridization is not occurring between eastern cottontails and New England or Appalachian cottontails. Limited variation in mitochondrial DNA does not support the recent reclassification of S. transitionalis into sister-species. However, karyotypic and morphological differences between northern and southern populations should be considered during any efforts to restore declining populations of this species.
We provide an updated distribution and dispersal rate of the European hare (Lepus europaeus Pallas, 1778) introduced in South America, with georeferenced record localities. According to our results the current geographic distribution of the European hare, would cover practically all of Argentina, Chile and Uruguay, southeastern Peru, southwestern Bolivia, southeastern Paraguay, and central part of southern Brazil. During the process of invading new areas, the hare has occupied very dissimilar environments, from the bushy steppes and Andean deserts of Bolivia and Peru to the dry and humid forests and wooded savannahs of Paraguay and Brazil. This would explain the variation observed in the dispersal rates that varied between 10 and 37 km/year.
Although species within Lagomorpha are derived from a common ancestor, the distribution range and body size of its two extant groups, ochotonids and leporids, are quite differentiated. It is unclear what has driven their disparate evolutionary history. In this study, we compile and update all fossil records of Lagomorpha for the first time, to trace the evolutionary processes and infer their evolutionary history using mitochondrial genes, body length and distribution of extant species. We also compare the forage selection of extant species, which offers an insight into their future prospects. The earliest lagomorphs originated in Asia and later diversified in different continents. Within ochotonids, more than 20 genera occupied the period from the early Miocene to middle Miocene, whereas most of them became extinct during the transition from the Miocene to Pliocene. The peak diversity of the leporids occurred during the Miocene to Pliocene transition, while their diversity dramatically decreased in the late Quaternary. Mantel tests identified a positive correlation between body length and phylogenetic distance of lagomorphs. The body length of extant ochotonids shows a normal distribution, while the body length of extant leporids displays a non-normal pattern. We also find that the forage selection of extant pikas features a strong preference for C3 plants, while for the diet of leporids, more than 16% of plant species are identified as C4 (31% species are from Poaceae). The ability of several leporid species to consume C4 plants is likely to result in their size increase and range expansion, most notably in Lepus. Expansion of C4 plants in the late Miocene, the so-called 'nature's green revolution', induced by global environmental change, is suggested to be one of the major 'ecological opportunities', which probably drove large-scale extinction and range contraction of ochotonids, but inversely promoted diversification and range expansion of leporids.
We examined the phylogenetic status and history of the mountain hare Lepus timidus in and around Hokkaido using mitochondrial cytochrome b (cyt b) sequences from 158 samples from Hokkaido and 14 from Sakhalin, as well as four samples from the Korean hare, L. coreanus. The phylogenetic analysis of the cyt b sequences generated in this study and obtained from DNA databases showed the clear genetic specificity of the Hokkaido lineage as a clade. The Hokkaido lineage was estimated to have diverged from the other conspecific and L. coreanus lineages 0.46 and 0.30 million years ago (Mya), respectively. These results suggest that the common ancestor of the mitochondrial lineage in Hokkaido and Korea inhabited Far East Asia before colonization by the present continental lineages of L. timidus, including the Sakhalin population. We estimated the time of the most recent common ancestor of the Hokkaido population to be 0.17 Mya, and found two distinct haplogroups within the island. One group had greater genetic diversity (mean number of pairwise differences: π = 0.0188 ± 0.0108) and appears to have expanded from the west to the entire island of Hokkaido. The other had lower genetic diversity (π = 0.0038 ± 0.0037) and its distribution was concentrated in the east. These contrasting west/east trends indicate that the Hokkaido population was fragmented in the past, and then subsequently expanded. Our study suggests that Hokkaido was an important refugium for boreal species in the far eastern region, and allowed the formation of various population genetic structures within the island.
This review highlights the status of the European wild rabbit Oryctolagus cuniculus , which is threatened within its native range and yet is a highly successful colonizer across its worldwide, introduced range.
The European wild rabbit is a keystone species in Iberia, and the survival of a range of threatened predator species, including the Iberian lynx Lynx pardinus and Spanish imperial eagle Aquila aldabertii , is dependent upon the restoration of rabbit populations. Although not native to the UK, the rabbit also performs significant ecosystem services for nationally rare UK species, by maintaining short sward heights in heathland and grassland ecosystems, and serving as a prey item for populations of predators.
We identify the European wild rabbit as an excellent model to demonstrate the wide range of complex effects that an introduced mammalian species may exert on ecosystems to which it has been introduced. These effects include habitat degradation following overgrazing, competition with native mammals and facilitating meso‐predator release and hyperpredation.
We also show that rabbit eradication from some sites may generate more problems than are solved because of the impacts of trophic cascades stemming from dependence on rabbits by native predator assemblages.
Aim To use the method of parsimony analysis of endemism to identify areas of endemism for passerine birds in the Atlantic Forest, South America, and to compare the locations of these areas with areas previously identified for birds as well as other taxa.
Location The Atlantic Forest, eastern South America.
Methods We analysed a matrix composed of the presence (1) or absence (0) of 140 endemic species in 24 quadrats of 1 × 1 degree distributed along the Atlantic Forest to find the most parsimonious area cladogram.
Results Fourteen most parsimonious cladograms were found and then summarized in a single consensus tree. Four areas of endemism were identified: Pernambuco, Central Bahia, Coastal Bahia, and Serra do Mar.
Main conclusions Avian areas of endemism in the Atlantic Forest have significant generality, as they are highly nonrandom and congruent with those of other groups of organisms. A first hypothesis about the historical relationships among the four areas of avian endemism in the Atlantic Forest is delineated. There is a basal dichotomy among areas of endemism in the Atlantic Forest, with Pernambuco forming a northern cluster and Coastal Bahia, Central Bahia and Serra do Mar comprising a southern cluster. Within the southern cluster, Central Bahia and Serra do Mar are more closely related to each other than to Coastal Bahia.
Abstract— The “soft” assumption attributes polytomies to lack of data, not simultaneous cladogenesis (the “hard” assumption). Most systematists prefer the first interpretation, but most parsimony programs implicitly use the second. Results can thus be inconsistent with initial assumptions. Under certain circumstances that seem especially typical for large data sets treating higher taxa, it may be valid to eliminate both compatible and incompatible polytomous trees from consideration. Consistent treatment of soft polytomies can reduce the ambiguity of cladistic solutions and improve the resolution, and testability, of phylogenetic hypotheses.
With the increasing availability of molecular data, maximum likelihood approaches have gained a new central role in phylogenetic reconstructions. Extremely fast tree-search algorithms have been developed to handle data sets of ample size in reasonable time. In the past few years, RAxML has achieved great relevance in this field and obtained wide distribution among evolutionary biologists and taxonomists because of its high computational performance and accuracy. However, there are certain drawbacks with regard to its usability, since the program is exclusively command-line based. To overcome this problem, we developed raxmlGUI, a graphical user interface that makes the use of RAxML easier and highly intuitive, enabling the user to perform phylogenetic analyses of varying complexity. The GUI includes all main options of RAxML, and a number of functions are automated
or simplified. In addition, some features extend the standard use of RAxML, like assembling concatenated alignments with automatic partitioning. RaxmlGUI is an open source Python program, available in a cross-platform package that incorporates RAxML executables for the main operating systems. It can be downloaded from http://sourceforge.net/projects/raxmlgui/.
Keywords: Rapid bootstrap; Graphical user interface; Maximum likelihood; Phylogenetic analyses; Python; RAxML
A new leporid species, Nesolagus sinensis sp. nov., is described here representing the only leporid member of the Early Pleistocene Gigantopithecus fauna from Sanhe Cave, Chongzuo, Guangxi, South China and also the first fossil taxon of the Southeast Asian genus Nesolagus. Compared with two extant Nesolagus species from Indonesia and Vietnam and other related leprids, the new species has a relatively small size and an extraordinarily
weak anterior internal reentrant (AIR) on p3, but it also retains the simplified paedomorphic pattern during the ontogenetic
process as in extant species, which suggests that the new species is more primitive than and probably directly ancestral to
extant Nesolagus species. The new species seems closely related to Alilepus longisinuosus from the Late Miocene strata of Lufeng, Yunnan, and probably diverged from a leporid similar to its ancestral form. It also
indicates that Nesolagus originated in Southwest China.
KeywordsGuangxi of China-Early Pleistocene-
Nesolagus sinensis sp. nov.-
Gigantopithecus fauna
Exotic mammals in South America represent about 20% of world mammal introductions. The aim of our paper is to provide a global
assessment of the exotic mammals of Argentina, their pathways, impacts, and a synthesis of their attributes as potential invasive
species. We reviewed and compiled data from a diversity of sources and databases on alien mammals occurring in feral state
exclusively. We recorded 18 species of exotic mammals for Argentina. The majority of introductions occurred between the 18th
and 19th centuries and their ports of entry were located in temperate ecosystems, between 34° and 55° SL. Most of their entry
pathways were associated with human activities (e.g. sport hunting, food and fur industry). The exotic mammals occupy ecoregions
similar to their original distributions, but most of them have experienced a range expansion to novel habitats. The fauna
of exotic mammals of Argentina represents a good opportunity to understand the dynamics of the invasion process as they represent
a diversity of ecological groups and environmental contexts.
Understanding the evolutionary history of living organisms is a central problem in biology. Until recently the ability to infer evolutionary relationships was limited by the amount of DNA sequence data available, but new DNA sequencing technologies have largely removed this limitation. As a result, DNA sequence data are readily available or obtainable for a wide spectrum of organisms, thus creating an unprecedented opportunity to explore evolutionary relationships broadly and deeply across the Tree of Life. Unfortunately, the algorithms used to infer evolutionary relationships are NP-hard, so the dramatic increase in available DNA sequence data has created a commensurate increase in the need for access to powerful computational resources. Local laptop or desktop machines are no longer viable for analysis of the larger data sets available today, and progress in the field relies upon access to large, scalable high-performance computing resources. This paper describes development of the CIPRES Science Gateway, a web portal designed to provide researchers with transparent access to the fastest available community codes for inference of phylogenetic relationships, and implementation of these codes on scalable computational resources. Meeting the needs of the community has included developing infrastructure to provide access, working with the community to improve existing community codes, developing infrastructure to insure the portal is scalable to the entire systematics community, and adopting strategies that make the project sustainable by the community. The CIPRES Science Gateway has allowed more than 1800 unique users to run jobs that required 2.5 million Service Units since its release in December 2009. (A Service Unit is a CPU-hour at unit priority).
A critical issue with species names derived from Linnaeus’ 10th edition of the Systema Naturae is the lack of holotypes, which in many instances has led to taxonomic confusion and uncertainty, as well as an unstable taxonomy. In the particular case of the South American cottontail, currently known as Sylvilagus brasiliensis, Linnaeus listed the type locality as “America Meridionali,” or South America. As a result, S. brasiliensis was ascribed a widespread distribution in North and South America, over an area estimated as approximately 1.09 × 107 Km2, and containing upwards of 37 named subspecies. In order to stabilize the taxonomy and initiate the process of illumination of evolutionary and biogeographic relationships among the South American cottontails, we designate herein a neotype for S. brasiliensis.
Lepus capensis pamirensis is a specific cape hare species that is only distributed in the Pamirs, with a cruel natural environment. The complete mitochondrial genome of the cape hare L. c. pamirensis was first determined (accession number LC073697), in a total length of 17 597 nucleotides, of which 15 310 nucleotides are coding DNA and 2287 nucleotides are non-coding DNA. It has the common feature with those of other hares with respect to genome structure and gene arrangement. It contained 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer tRNA genes and 1 control region (D-loop region). The complete mitochondrial genome of the cape hare L. c. pamirensis provides an important data set for further study on its classification.
Phylogenomics has largely succeeded in its aim of accurately inferring species trees, even when there are high levels of discordance among individual gene trees. These resolved species trees can be used to ask many questions about trait evolution, including the direction of change and number of times traits have evolved. However, the mapping of traits onto trees generally uses only a single representation of the species tree, ignoring variation in the gene trees used to construct it. Recognizing that genes underlie traits, these results imply that many traits follow topologies that are discordant with the species topology. As a consequence, standard methods for character mapping will incorrectly infer the number of times a trait has evolved. This phenomenon, dubbed "hemiplasy," poses many problems in analyses of character evolution. Here we outline these problems, explaining where and when they are likely to occur. We offer several ways in which the possible presence of hemiplasy can be diagnosed, and discuss multiple approaches to dealing with the problems presented by underlying gene tree discordance when carrying out character mapping. Finally, we discuss the implications of hemiplasy for general phylogenetic inference, including the possible drawbacks of the widespread push for "resolved" species trees. This article is protected by copyright. All rights reserved.
Geographic variation in Sylvilagus brasiliensis and S. insonus from Mexico and Central America was reviewed by univariate and multivariate techniques. Rabbits currently referred to S. brasiliensis from the Cordillera de Talamanca of Costa Rica and Panama are referable to a distinct species, S. dicei Harris, 1932. Sylvilagus brasiliensis occurs in the eastern and southern lowland tropics of Mexico south through Panama and is composed of two well-defined subspecies, S. b. truei and S. b. gabbi, with a sharp zone of intergradation in southern Chiapas and Guatemala. Sylvilagus b. consobrinus, S. b. messorius, S. b. tumacus, and S. b. incitatus are all regarded as synonyms of S. h. gabbi. Comparisons of the species S. brasiliensis, S. dicei, and S. insonus indicate that S. brasiliensis and S. dicei are more closely related than either is to S. insonus.
In order to elucidate the systematic relevance of the turbinal skeleton in Lagomorpha the ethmoidal regions of 6 ochotonid, 21 leporid, and 2 outgroup species (Sciurus vulgaris, Tupaia sp.) species were investigated by high-resolution computed tomography (μCT). Number and shape of turbinals correspond to major clades and to several genera. All Lagomorpha under study have a deeply excavated nasoturbinal that is continuous with the lamina semicircularis; a feature likely to be an autapomorphy of lagomorphs. In particular, the olfactory turbinals (frontoturbinals, ethmoturbinals, and interturbinals) provide new systematic information. The plesiomorphic lagomorph pattern comprises two frontoturbinals, three ethmoturbinals, and one interturbinal between ethmoturbinal I and II. Ochotonidae are derived from the lagomorph goundplan by loss of ethmoturbinal III; an interturbinal between the two frontoturbinals is an autapomorphy of Leporidae. Pronolagus is apomorphic in having a very slender first ethmoturbinal, but shows a puzzling pattern in decreasing the number of turbinals. Pronolagus rupestris and Romerolagus diazi have independently reduced their turbinals to just two fronto- and two ethmoturbinals, which is the lowest number among the sampled lagomorphs. In contrast, the more derived leporid genera under study (Oryctolagus, Caprolagus, Sylvilagus, and Lepus) show a tendency to increase the number of turbinals, either by developing an ethmoturbinal IV (Caprolagus hispidus, Lepus arcticus) or by additional interturbinals. Intraspecific variation was investigated in Ochotona alpina, Oryctolagus cuniculus, and Lepus europaeus and is restricted to additional interturbinals in the frontoturbinal recess of the two leporids. Anat Rec, 297:2031–2046, 2014. © 2014 Wiley Periodicals, Inc.
ABSTRACT We review current knowledge of the evolutionary relationships among species of Leporidae drawing on molecular, cytogenetic and morphological data. We highlight problems associated with retrieving phylogenetic information under conditions of a rapid radiation and the lack of phylogenetically informative cytogenetic and mitochondrial DNA characters. Most morphological features underpinning generic distinctions are subtle and prone to reversal and convergence and as a consequence, they generally provide little basis for assessing phylogenetic affinity. We report the results of a supermatrix analysis that combines published nucleotide sequence data, unique insertion/deletion events, morphological characters and presumed geographical centres of origin of each genus. This represents the most comprehensive intergeneric comparison of the Leporidae thus far undertaken. The monophyly of the 11 leporid genera is unambiguously supported. There is support for an Afroasian assemblage that comprises Poelagus, Pronolagus and Nesolagus, a primitive Lepus, with the problematic Bunolagus, Oryctolagus, Caprolagus and Pentalagus as derived species in a clade that also includes the closely related Brachylagus and Sylvilagus as sister taxa. There is no support for the Palaeolaginae, although Romerolagus is an ancient lineage within the extant Leporidae. We hold that of the polytypic genera Lepus remains the most problematic, and provide a working hypothesis that will hopefully encourage future research on the various hare species.