Eliécer E. Gutiérrez

Molecular Systematics of Mouse Opossums (Didelphidae: Marmosa): Assessing Species Limits using Mitochondrial DNA Sequences, with Comments on Phylogenetic Relationships and Biogeography

Abstract The genus Marmosa contains 15 currently recognized species, of which nine are referred to the subgenus Marmosa, and six to the subgenus Micoureus. Recent revisionary research based on morphological data, however, suggests that the subgenus Marmosa is more diverse than the currently accepted taxonomy indicates. Herein we report phylogenetic analyses of sequence data from the mitochondrial cytochrome-b gene representing 12 of the 14 morphologically defined taxa recently treated as valid species of Marmosa (Marmosa) in the aforementioned revisionary work. These data provide a basis for testing the monophyly of morphologically defined taxa in the subgenus Marmosa, and they afford the first opportunity to assess phylogenetic relationships among the majority of species currently referred to the genus. Ten of 11 species of Marmosa (Marmosa) represented by multiple sequences in our analyses were recovered as monophyletic. In contrast, our samples of M. mexicana were recovered as two deeply divergent haplogroups that were not consistently associated as sister taxa. Among other results, our analyses support the recognition of M. isthmica and M. simonsi as species distinct from M. robinsoni, and the recognition of M. macrotarsus and M. waterhousei as species distinct from M. murina. The validity of three other species long recognized as distinct (M. rubra, M. tyleriana, and M. xerophila) is also clearly supported by our results. Although cytochrome-b sequence data are not consistently informative about interspecific relationships in this study, we found strong support for several clades, including (1) the subgenus Micoureus; (2) a group comprised of Marmosa macrotarsus, M. murina, M. tyleriana, and M. waterhousei; (3) a group comprised of M. robinsoni and M. xerophila; and (4) a group comprising all of the species in the subgenus Marmosa that occur north and west of the Andes (M. isthmica, M. mexicana, M. robinsoni, M. simonsi, M. xerophila, and M. zeledoni). Our discovery of the latter clade suggests that the Andes may have played a major role in the early diversification of this speciose radiation of small Neotropical marsupials.

In-solution hybridization for mammalian mitogenome enrichment: pros, cons and challenges associated with multiplexing degraded DNA

Here, we present a set of RNA‐based probes for whole mitochondrial genome in‐solution enrichment, targeting a diversity of mammalian mitogenomes. This probes set was designed from seven mammalian orders and tested to determine the utility for enriching degraded DNA. We generated 63 mitogenomes representing five orders and 22 genera of mammals that yielded varying coverage ranging from 0 to >5400X. Based on a threshold of 70% mitogenome recovery and at least 10× average coverage, 32 individuals or 51% of samples were considered successful. The estimated sequence divergence of samples from the probe sequences used to construct the array ranged up to nearly 20%. Sample type was more predictive of mitogenome recovery than sample age. The proportion of reads from each individual in multiplexed enrichments was highly skewed, with each pool having one sample that yielded a majority of the reads. Recovery across each mitochondrial gene varied with most samples exhibiting regions with gaps or ambiguous sites. We estimated the ability of the probes to capture mitogenomes from a diversity of mammalian taxa not included here by performing a clustering analysis of published sequences for 100 taxa representing most mammalian orders. Our study demonstrates that a general array can be cost and time effective when there is a need to screen a modest number of individuals from a variety of taxa. We also address the practical concerns for using such a tool, with regard to pooling samples, generating high quality mitogenomes and detail a pipeline to remove chimeric molecules.

Phylogenetic Relationships of Mouse Opossums (Didelphidae, Marmosa) with a Revised Subgeneric Classification and Notes on Sympatric Diversity

ABSTRACT To resolve phylogenetic relationships among species of Marmosa we analyzed DNA sequences from one mitochondrial and three nuclear genes for every member of the nominotypical subgenus and from four species of the subgenus Micoureus. As reported in previous studies, the subgenus Marmosa was found to be paraphyletic, whereas Micoureus was recovered as a robustly supported clade. Species currently referred to the subgenus Marmosa form four strongly supported and morphologically diagnosable groups. Based on these results we recognize a total of five subgenera: Marmosa Gray, 1821 (for macrotarsus, murina, tyleriana, and waterhousei); Micoureus Lesson, 1842 (for alstoni, constantiae, demerarae, paraguayana, phaea, and regina); Stegomarmosa Pine, 1972 (for andersoni and lepida); Eomarmosa, new subgenus (for rubra); and Exulomarmosa, new subgenus (for isthmica, mexicana, robinsoni, simonsi, xerophila, and zeledoni). The best-supported hypothesis of relationships among these clades is ((Stegomarmosa (Marmosa + Micoureus)) (Eomarmosa + Exulomarmosa)), and our results additionally resolve many interspecific relationships within each subgenus. These clades have broadly overlapping geographic distributions, especially in western Amazonia, where the arboreal insectivorous-frugivorous niche of Marmosa is apparently partitioned among multiple sympatric congeners.

Morphometrics and Taxonomy of Bats of the Genus Pteronotus (Subgenus Phyllodia) in Venezuela

Abstract In Venezuela, bats of the subgenus Phyllodia of the genus Pteronotus (Mormoopidae) are divided into 3 taxa, Pteronotus parnellii fuscus, P. p. paraguanensis, and P. p. rubiginosus. We compare them with respect to body size and shape by means of principal components analyses and cluster analyses applied to 26 craniodental and 7 appendicular (fore and rear limbs) measurements of 267 Venezuelan specimens. The analyses indicate that the subspecies endemic to the Península de Paraguaná, P. p. paraguanensis, differs from the other 2 taxa in being considerably smaller and in having markedly distinct craniodental and appendicular shapes; and, although to a lesser degree, P. p. fuscus and P. p. rubiginosus also differ notably from each other in these morphometric aspects. Our results justify raising P. p. paraguanensis to species rank. The tight dependence of members of Phyllodia on forest may explain the high levels of morphometric (this paper) and molecular (previous studies) variability of the subgenus. The reduced geographic distribution, small population, and full species status of the Phyllodia of Península de Paraguaná justify special conservation measures.

Chapter 2. Taxonomy, Distribution, and Natural History of the Genus Heteromys (Rodentia: Heteromyidae) in Central and Eastern Venezuela, with the Description of a New Species from the Cordillera de la Costa

Abstract Heteromys anomalus is widely distributed along the Caribbean coast of South America and had been considered the only spiny pocket mouse present in Venezuela for several decades. Recent taxonomic studies in western Venezuela, however, have documented the presence of H. australis from the Cordillera de Mérida and described H. oasicus from the Península de Paraguaná. Here, we revise the genus Heteromys in central and eastern Venezuela as well as in Trinidad and Tobago. Morphological comparisons with samples of H. anomalus from throughout its known range in Venezuela and with representatives of all other recognized species of the genus indicate the existence of a species new to science, which we describe as Heteromys catopterius (the Overlook Spiny Pocket Mouse). This species ranges from 350 to 2425 m in elevation in the Cordillera de la Costa in northern Venezuela, with the vast majority of records above ca. 700 m. In central and eastern Venezuela, H. anomalus is found in the surrounding lowlands and lower slopes of the Cordillera. Externally, H. catopterius is darker than H. anomalus and lacks the distinctly rounded ears of that species. The new species averages larger than H. anomalus for most external and cranial measurements. Cranially, the two species have differences in proportion; the skulls of H. catopterius are proportionately wider (less elongated) than those of H. anomalus, with a relatively wider interorbital constriction, wider interparietal, and more inflated braincase. Heteromys catopterius occurs in wet montane forests (especially cloud forests) in four highland areas of the Cordillera de la Costa: the main Aragua-Carabobo chain, the El Ávila massif, the Serranía del Interior, and the Macizo Oriental. Presumably, the warm, dry lowlands of the Depresión de Unare represent a barrier for the species, separating populations in the Macizo Oriental from the more westerly populations. Large areas of the known ranges of both H. catopterius and H. anomalus are protected in the Venezuelan network of protected areas.

Photography-based taxonomy is inadequate, unnecessary, and potentially harmful for biological sciences

The question whether taxonomic descriptions naming new animal species without type specimen(s) deposited in collections should be accepted for publication by scientific journals and allowed by the Code has already been discussed in Zootaxa (Dubois & Nemésio 2007; Donegan 2008, 2009; Nemésio 2009a-b; Dubois 2009; Gentile & Snell 2009; Minelli 2009; Cianferoni & Bartolozzi 2016; Amorim et al. 2016). This question was again raised in a letter supported by 35 signatories published in the journal Nature (Pape et al. 2016) on 15 September 2016. On 25 September 2016, the following rebuttal (strictly limited to 300 words as per the editorial rules of Nature) was submitted to Nature, which on 18 October 2016 refused to publish it. As we think this problem is a very important one for zoological taxonomy, this text is published here exactly as submitted to Nature, followed by the list of the 493 taxonomists and collection-based researchers who signed it in the short time span from 20 September to 6 October 2016.

Faunal nestedness and species-area relationship for small non-volant mammals in "sky islands" of northern Venezuela

We study the biogeography of small non-volant mammals in mesic montane sky islands of northern Venezuela. Fieldwork, examination of museum specimens, and critical use of literature yielded species lists for the Cordillera de Mérida, Cordillera de la Costa, Serranía de San Luis, and Cerro Santa Ana. Fieldwork confirmed the species known from Cerro Santa Ana and added 12 species for the Serranía de San Luis. Richness decreases with smaller area. Furthermore, the faunas are highly nested, with taxa dropping out at successive depressions. Species deviating from nestedness provide a signal indicative of in situ speciation in rodents but not in marsupials.

The mammalian faunas endemic to the Cerrado and the Caatinga

Abstract We undertook a comprehensive, critical review of literature concerning the distribution, conservation status, and taxonomy of species of mammals endemic to the Cerrado and the Caatinga, the two largest biomes of the South American Dry-Diagonal. We present species accounts and lists of species, which we built with criteria that, in our opinion, yielded results with increased scientific rigor relative to previously published lists – e.g., excluding nominal taxa whose statuses as species have been claimed only on the basis of unpublished data, incomplete taxonomic work, or weak evidence. For various taxa, we provided arguments regarding species distributions, conservation and taxonomic statuses previously lacking in the literature. Two major findings are worth highlighting. First, we unveil the existence of a group of species endemic to both the Cerrado and the Caatinga (i.e., present in both biomes and absent in all other biomes). From the biogeographic point of view, this group, herein referred to as Caatinga-Cerrado endemics, deserves attention as a unit – just as in case of the Caatinga-only and the Cerrado-only endemics. We present preliminary hypotheses on the origin of these three endemic faunas (Cerrado-only, Caatinga-only, and Caatinga-Cerrado endemics). Secondly, we discovered that a substantial portion of the endemic mammalian faunas of the Caatinga and the Cerrado faces risks of extinction that are unrecognized in the highly influential Red List of Threatened Species published by the International Union for Conservation of Nature (IUCN). “Data deficient” is a category that misrepresents the real risks of extinction of these species considering that (a) some of these species are known only from a handful of specimens collected in a single or a few localities long ago; (b) the Cerrado and the Caatinga have been sufficiently sampled to guarantee collection of additional specimens of these species if they were abundant; (c) natural habitats of the Cerrado and the Caatinga have been substantially altered or lost in recent decades. Failures either in the design of the IUCN criteria or in their application to assign categories of extinction risks represent an additional important threat to these endemic faunas because their real risks of extinctions become hidden. It is imperative to correct this situation, particularly considering that these species are associated to habitats that are experiencing fast transformation into areas for agriculture, at an unbearable cost for biodiversity.

The Taxonomic Status of Mazama bricenii and the Significance of the Táchira Depression for Mammalian Endemism in the Cordillera de Mérida, Venezuela.

We studied the taxonomy and biogeography of Mazama bricenii, a brocket deer classified as Vulnerable by the IUCN, drawing on qualitative and quantitative morphology and sequences of the mitochondrial cytochrome-b gene. We used Ecological Niche Modeling (ENM) to evaluate the hypothesis that M. bricenii of the Venezuelan Cordillera de Mérida (CM) might have become isolated from populations of its putative sister species, Mazama rufina, in the Colombian Cordillera Oriental (CO). This hypothesis assumes that warm, dry climatic conditions in the Táchira Depression were unsuitable for the species. Our analyses did not reveal morphological differences between specimens geographically attributable to M. bricenii and M. rufina, and phylogenetic analyses of molecular data recovered M. bricenii nested within the diversity of M. rufina. These results indicate that M. bricenii should be regarded as a junior synonym of M. rufina. ENM analyses revealed the existence of suitable climatic conditions for M. rufina in the Táchira Depression during the last glacial maximum and even at present, suggesting that gene flow between populations in the CO and CM may have occurred until at least the beginning of the current interglacial period and may continue today. Because this pattern might characterize other mammals currently considered endemic to the CM, we examined which of these species match two criteria that we propose herein to estimate if they can be regarded as endemic to the CM with confidence: (1) that morphological or molecular evidence exists indicating that the putative endemic taxon is distinctive from congeneric populations in the CO; and (2) that the putative endemic taxon is restricted to either cloud forest or páramo, or both. Only Aepeomys reigi, Cryptotis meridensis, and Nasuella meridensis matched both criteria; hence, additional research is necessary to assess the true taxonomic status and distribution of the remaining species thought to be CM endemics.

Phylogeography of Marmosa robinsoni: insights into the biogeography of dry forests in northern South America

Abstract Robinsons mouse opossum (Marmosa robinsoni) typically inhabits xeric shrublands, savannas, and deciduous forests from Panama through Colombia and Venezuela, to the islands of Trinidad, Tobago, and Grenada. We assessed its phylogeographic structure in the 1st such study based on dense geographic sampling of any vertebrate from dry habitats in this region. We sequenced the cytochrome-b gene and the X-linked intron O-linked N-acetylglucosamine transferase, largely from dried skins and residual tissue on osteological material of museum specimens. Phylogenetic analyses revealed the existence of 2 well-supported phylogroups primarily distributed to the east and west of the Cordillera de Mérida. The estimated time since divergence between these phylogroups postdates the Miocene; therefore, Andean uplifts, changes in the course of the Río Orinoco, and marine transgressions of that epoch cannot be implicated as causal vicariant agents. Instead, expansion of humid forest or marine transgressions, or both, during the Pliocene and Pleistocene more likely led to this differentiation. We encountered little structure among populations east of the Cordillera de Mérida, suggesting recent range expansion in this region. Surprisingly, isolated populations from the Península de Paraguaná (northwestern Venezuela) are not closely related to geographically proximate mainland populations, but rather to more distant populations to the west in Colombia and Panama. By contrast, populations from central and eastern Venezuela are closely related to those on the islands of Trinidad and Tobago. This genetic similarity among currently disjunct populations of M. robinsoni might have resulted from Holocene fragmentation of a more extensive Pleistocene distribution on coastal plains that were exposed during the last glacial maximum. Resumen Marmosa robinsoni típicamente habita arbustales secos, sabanas, y bosques deciduos de Panamá, Colombia, y Venezuela, y se encuentra presente también en las islas de Trinidad, Tobago, y Granada. En este estudio evaluamos la estructura filogeográfica de M. robinsoni en lo que, hasta donde sabemos, representa el primer estudio de este tipo basado en un muestreo geográfico denso de un vertebrado de los hábitats secos del norte de Suramérica. Secuenciamos el gen mitocondrial citocromo b y el intron nuclear O-N-acetilglucosamina transferasa (ubicado en el cromosoma X). Para ello, obtuvimos ADN principalmente a partir de pieles de estudio y tejido residual tomado de material osteológico de ejemplares de museos. Los análisis filogenéticos revelaron (con buen apoyo) la existencia de dos filogrupos predominantemente distribuidos al Este y Oeste de la Cordillera de Mérida. La estimación del tiempo transcurrido desde que estos dos filogrupos divergieron claramente indica que tal divergencia ocurrió luego del Mioceno; por lo tanto, el levantamiento de los Andes, los cambios de curso del Río Orinoco, y las transgresiones marinas de esa época no pueden ser consideradas como posibles agentes vicariantes relevantes entre estos grupos. En cambio, expansiones de bosques húmedos y/o transgresiones marinas durante el Plioceno y Pleistoceno podrían haber causado esta divergencia. Encontramos poca estructura filogeográfica entre las poblaciones al Este de la Cordillera de Mérida, lo cual sugiere una expansión reciente a esta región. Sorprendentemente, poblaciones aisladas en la Península de Paraguaná (noroeste de Venezuela) no están cercanamente relacionadas con las poblaciones geográficamente más próximas (continentales y adyacentes a la península), sino a las poblaciones más distantes al Oeste en Colombia y Panamá. En cambio, las poblaciones del centro y del oriente de Venezuela están cercanamente relacionadas a poblaciones presentes en las islas Trinidad y Tobago. Esta similitud genética entre poblaciones disyuntas podría haberse originado en el Holoceno, posiblemente por la fragmentación de una distribución más amplia de M. robinsoni durante el fin del Pleistoceno, cuando la especie podría haber ocupado planicies costeras expuestas por el último máximo glacial.