Body mass data set for 1,317 bird and 270 mammal species from Colombia.

Body mass is one of the most important phenotypic attributes in animal ecology and life history. This trait is widely used in the fields of ecology and macroevolution, since it influences physiology, morphological functions, and a myriad of ecological and social interactions. In this data set, our aim was to gather a comprehensive bird and mammal body mass data set from northern South America. We report body mass, discriminated by sex, for 42,022 individual birds and 7,441 mammals representing 1,317 bird species (69% of Colombia's avifauna) and 270 mammal species (51% of Colombian mammals) from the Neotropics. The data were sourced from vouchers collected between 1942 and 2020 and from individuals captured and released at banding stations over the last two decades for birds (2000-2020) and the last decade for mammals (2010-2020), by 10 research groups and institutions in Colombia. This data set fills gaps identified in other similar databases, as it focuses on northern South America, a highly diverse Neotropical region often underrepresented in morphological data sets. We provide wide taxonomic coverage for studies interested in information both at regional and local scales. There are no copyright restrictions; the present data paper should be appropriately cited when data are used for publication. The authors would appreciate learning about research projects, teaching exercises, and other uses given to this data set and are open to contribute in further collaborations using these data.

RELICT HUMID TROPICAL FOREST IN MEXICO PROMOTES DIFFERENTIATION IN BARRED WOODCREEPERS Dendrocolaptes (AVES: FURNARIIDAE).

Humid tropical forests in Mesoamerica are distributed along the Atlantic slope and, in scattered locations, along the Mexican Pacific slope. These poorly explored Mexican forests include microendemic bird species. Two species in the genus Dendrocolaptes occur in lowland and foothill humid tropical forests of Mesoamerica. One of these, D. sanctithomae, is comprised of four subspecies, of which the two that occur in Mexico, D. s. sanctithomae and D. s. sheffleri, are distinctly different morphologically, and the latter is a poorly known microendemic taxon of the Mexican Pacific humid tropical forest in the Sierra Madre del Sur. We used both nuclear (nDNA) and mitochondrial DNA (mtDNA) to evaluate the genetic variation of D. sanctithomae in Mexico, and complemented this with a quantitative analysis of phenotypic traits. We also conducted analyses of environmental niche models to test the hypothesis of niche differentiation of D. s. sheffleri from other taxa of D. sanctithomae. Our phylogenetic reconstructions of mtDNA consistently recovered D. s. sheffleri and D. s. sanctithomae as reciprocally monophyletic, while they shared alleles of nDNA. These mtDNA differences are comparable with differences reported between other Dendrocolaptes sister-taxa pairs. Our analysis of phenotypic traits also indicated that the taxa differ in measurements of hallux and feather barring. In contrast, niche differentiation tests suggest that the niches of both taxa are more similar than expected by chance. Our evidence leads us to propose species status for D. sheffleri. This is an additional example of recent speciation in Mexico that indicates active and peripatric evolutionary differentiation in the northern Neotropics.

Sobre las aves de las expediciones Santander-Bio, cuantificando el costo de colectar especímenes en Colombia / On birds of santander-bio expeditions, quantifying the cost of collecting voucher specimens in colombia

ABSTRACT Several scientific reasons support continuing bird collection in Colombia, a megadiverse country with modest science financing. Despite the recognized value of biological collections for the rigorous study of biodiversity, there is scarce information on the monetary costs of specimens. We present results for three expeditions conducted in Santander (municipalities of Cimitarra, El Carmen de Chucurí, and Santa Barbara), Colombia, during 2018 to collect bird voucher specimens, quantifying the costs of obtaining such material. After a sampling effort of 1290 mist net hours and occasional collection using an airgun, we collected 300 bird voucher specimens, representing 117 species from 30 families. Such collection represents one of the largest series obtained during the historical ornithological exploration of Santander. We report differences among expeditions regarding the capture rate in mist nets, as well as differences in the sizes of taxa collected by mist nets and airgun. We discuss results in the context of previous ornithological expeditions in Colombia, commenting issues on the biology of some species, particularly those considered as noteworthy records (e.g., Red-legged Tinamou [Crypturellus erythropus], Cinnamon Screech Owl [Megascopspetersoni], Saffron-headed Parrot [Pyriliapyrilia], Black Inca [Coeligena prunellei], and Chestnut-crowned Gnateater [Conopophaga castaneiceps]). We calculated that the costs of obtaining and curating a specimen in Colombia, including tissues for molecular analysis, was ~US$60.4 (~$196 176 COP), which is among published costs of obtaining voucher specimens in other taxa and countries. These costs must be considered an investment in scientific capital because voucher specimens will provide biological information for hundreds of years.

RESUMEN Hay distintas razones científicas que apoyan la recolección de aves en Colombia, un país megadiverso pero con una modesta inversión en ciencia. Pese al valor de las colecciones biológicas para el estudio riguroso de la biodiversidad, la información sobre costos monetarios de recolectar especímenes es escasa. Presentamos resultados de la cuantificación del costo de obtener especímenes de aves durante tres expediciones en Santander (municipios de Cimitarra, El Carmen de Chucurí y Santa Bárbara), Colombia, en 2018. Tras un esfuerzo de muestreo de 1290 horas/red y recolecta ocasional con una pistola de aire, obtuvimos 300 especímenes pertenecientes a 117 especies de 30 familias, una de las series más grandes de la historia de la exploración ornitológica del departamento de Santander. Reportamos diferencias entre expediciones en cuanto a la tasa de captura con redes de niebla, así como diferencias en los tamaños de los taxones recolectados mediante redes de niebla y pistola de aire. Discutimos los resultados en el contexto de otras expediciones ornitológicas en Colombia, comentando algunos aspectos de la biología de especies relevantes (e.g., Crypturellus erythropus, Megascops petersoni, Pyrilia pyrilia, Coeligena prunellei y Conopophaga castaneiceps). El costo que calculamos para obtener y curar un espécimen, incluyendo tejidos para análisis moleculares futuros, es de ~$60,4 dólares estadounidenses (~$196 176 pesos colombianos), costo que se encuentra dentro del rango para obtener especímenes de otros taxones en otros países. Estos costos deben considerarse como una inversión al capital científico, debido a que los especímenes brindarán información biológica por cientos de años.

Phylogeography indicates incomplete genetic divergence among phenotypically differentiated montane forest populations of Atlapetesalbinucha (Aves, Passerellidae).

The White-naped Brushfinch (Atlapetesalbinucha) comprises up to eight allopatric subspecies mainly identified by the color of the underparts (gray vs. yellow belly). Yellow and gray bellied forms were long considered two different species (A.albinucha and A.gutturalis), but they are presently considered as one polytypic species. Previous studies in the genus Atlapetes have shown that the phylogeny, based on molecular data, is not congruent with characters such as coloration, ecology, or distributional patterns. The phylogeography of A.albinucha was analyzed using two mitochondrial DNA regions from samples including 24 different localities throughout montane areas from eastern Mexico to Colombia. Phylogeographic analyses using Bayesian inference, maximum likelihood and haplotype network revealed incomplete geographic structure. The genetic diversity pattern is congruent with a recent process of expansion, which is also supported by Ecological Niche Models (ENM) constructed for the species and projected into three past scenarios. Overall, the results revealed an incomplete genetic divergence among populations of A.albinucha in spite of the species' ample range, which contrasts with previous results of phylogeographic patterns in other Neotropical montane forest bird species, suggesting idiosyncratic evolutionary histories for different taxa throughout the region.

The niche and phylogeography of a passerine reveal the history of biological diversification between the Andean and the Atlantic forests.

The Atlantic Forest is separated from the Andean tropical forest by dry and open vegetation biomes (Chaco and Cerrado). Despite this isolation, both rainforests share closely related lineages, which suggest a past connection. This connection could have been important for forest taxa evolution. In this study, we used the Saffron-billed Sparrow (Arremon flavirostris) as a model to evaluate whether the Andean and the Atlantic forests act as a refugia system, as well as to test for a history of biogeographic connection between them. In addition, we evaluated the molecular systematic of intraspecific lineages of the studied species. We modeled the current and past distribution of A. flavirostris, performed phylogeographic analyses based on mitochondrial and nuclear genes, and used Approximate Bayesian Computation (ABC) analyses to test for biogeographic scenarios. The major phylogeographic disjunction within A. flavirostris was found between the Andean and the Atlantic forests, with a divergence that occurred during the Mid-Pleistocene. Our paleodistribution models indicated a connection between these forest domains in different periods and through both the Chaco and Cerrado. Additionally, the phylogeographic and ABC analyses supported that the Cerrado was the main route of connection between these rainforests, but without giving decisive evidence against a Chaco connection. Our study with A. flavirostris suggest that the biodiversity of the Andean and of the Atlantic forests could have been impacted (and perhaps enriched?) by cycles of connections through the Cerrado and Chaco. This recurrent cycle of connection between the Andean and the Atlantic Forest could have been important for the evolution of Neotropical forest taxa. In addition, we discussed taxonomic implications of the results and proposed to split the studied taxon into two full species.

On the importance of geographic and taxonomic sampling in phylogeography: A reevaluation of diversification and species limits in a Neotropical thrush (Aves, Turdidae).

Phylogeographic studies seeking to describe biogeographic patterns, infer evolutionary processes, and revise species-level classification should properly characterize the distribution ranges of study species, and thoroughly sample genetic variation across taxa and geography. This is particularly necessary for widely distributed organisms occurring in complex landscapes, such as the Neotropical region. Here, we clarify the geographic range and revisit the phylogeography of the Black-billed Thrush (Turdus ignobilis), a common passerine bird from lowland tropical South America, whose evolutionary relationships and species limits were recently evaluated employing phylogeographic analyses based on partial knowledge of its distribution and incomplete sampling of populations. Our work employing mitochondrial and nuclear DNA sequences sampled all named subspecies and multiple populations across northern South America, and uncovered patterns not apparent in earlier work, including a biogeographic interplay between the Amazon and Orinoco basins and the occurrence of distinct lineages with seemingly different habitat affinities in regional sympatry in the Colombian Amazon. In addition, we found that previous inferences about the affinities and taxonomic status of Andean populations assumed to be allied to populations from the Pantepui region were incorrect, implying that inferred biogeographic and taxonomic scenarios need re-evaluation. We propose a new taxonomic treatment, which recognizes two distinct biological species in the group. Our findings illustrate the importance of sufficient taxon and geographic sampling to reconstruct evolutionary history and to evaluate species limits among Neotropical organisms. Considering the scope of the questions asked, advances in Neotropical phylogeography will often require substantial cross-country scientific collaboration.

The database of the PREDICTS (Projecting Responses of Ecological Diversity In Changing Terrestrial Systems) project.

The PREDICTS project-Projecting Responses of Ecological Diversity In Changing Terrestrial Systems (www.predicts.org.uk)-has collated from published studies a large, reasonably representative database of comparable samples of biodiversity from multiple sites that differ in the nature or intensity of human impacts relating to land use. We have used this evidence base to develop global and regional statistical models of how local biodiversity responds to these measures. We describe and make freely available this 2016 release of the database, containing more than 3.2 million records sampled at over 26,000 locations and representing over 47,000 species. We outline how the database can help in answering a range of questions in ecology and conservation biology. To our knowledge, this is the largest and most geographically and taxonomically representative database of spatial comparisons of biodiversity that has been collated to date; it will be useful to researchers and international efforts wishing to model and understand the global status of biodiversity.

Colombian froze biodiversity: 16 years of the tissue collection of the humboldt intiitute / La biodiversidad congelada de Colombia: 16 años de la colección de tejidos del Instituto Humboldt

Collections of frozen tissue samples stand as keystone sources of molecular information to construct biodiversity knowledge, and are particularly challenged if they focus on megadiverse countries. In 1998 the Humboldt Institute (Instituto de Investigación de Recursos Biológicos Alexander von Humboldt) began a tissue collection of Colombian biodiversity (IAvH-CT) and the aim of this work is to present a diagnostic and an historical perspective for that collection, constructed by compiling information and experiences on its management as well as by organizing and curating the information of each catalogued sample. After 16 years, the IAvH-CT harbors 16,469 samples, which represent around 2530 species from 1289 genera, and 323 families of the Colombian biodiversity. Samples are biased toward plants (44 %) and birds (40 %), but also include other animal taxa. Geographically, IAvH-CT includes samples from all Colombian departments, but there is broad variation in their coverage. When compared with other international collections, IAvH-CT fulfills several standards of sample storage and data management, but its major weakness is that several tissues seem to lack a vouchered specimen. Tissues housed at IAvH-CT have been included in at least 48 studies published in several scientific journals. IAvH-CT is implementing strategies to improve curatorial standards, fill-in taxonomic gaps, and to explore the potential of its samples to understand the outstanding Colombian biota in a cooperative research framework among institutions.

Las colecciones de tejidos son fuentes fundamentales de información molecular para el conocimiento de la biodiversidad, y son particularmente desafiantes si están enfocadas en países megadiversos. En 1998 el Instituto Humboldt (Instituto de Investigación de Recursos Biológicos Alexander von Humboldt) inició una colección de tejidos de la biodiversidad colombiana (IAvH-CT). El objetivo de este trabajo es presentar un diagnóstico y una perspectiva histórica de esta colección, mediante la compilación de información y de experiencias sobre su manejo y organizando y curando la información de cada muestra catalogada. Después de 16 años IAvH-CT resguarda 16,469 muestras, que representan alrededor de 2530 especies de 1289 géneros y 323 familias de la biodiversidad colombiana. El número de muestras está sesgado hacia plantas (44 %) y aves (40 %), pero también incluyen otros taxones animales. Geográficamente, IAvH-CT incluye muestras de todos los departamentos colombianos, pero hay una gran variación en su cobertura. Al ser comparada con otras colecciones internacionales se encuentra que IAvH-CT cumple varios estándares de almacenamiento de muestras y de manejo de datos, pero su gran debilidad es que varios tejidos aparentemente carecen de un ejemplar de referencia. Varios tejidos almacenados en IAvH-CT han sido incluidos en al menos 48 estudios publicados en varias revistas científicas. IAvH-CT está implementando estrategias para mejorar la curaduría, llenar vacíos taxonómicos y explorar el potencial de sus muestras para entender la impresionante biota colombiana en un marco de investigación en cooperación con otras instituciones.

Patrones de la oomposición de aves acuáticas enel río la vieja, valle geográfiico del río cauca, Colombia / Composition Patterns of Waterbirds from La Vieja River, Geographic Valley of Cauca River, Colombia

Compilamos y analizamos los datos de observaciones realizadas entre los años 2001 y 2013 en tres sectores a lo largo del cauce del río La Vieja, ubicado en el valle geográfico del río Cauca, Colombia. Describimos los datos espacial y temporalmente, enfocándonos en identificar patrones de composición y abundancia de especies. Registramos 28 especies de aves acuáticas en 33 transectos, siendo 22 especies observadas en más del 50 % de los transectos. Las diferencias en el número de especies por transecto no fueron significativas entre los tres sectores del río. Sin embargo, dos análisis de agrupamiento, considerando tanto los datos de presencia/ausencia como de abundancia, indicaron que la composición de especies presenta estructura espacial a lo largo del río. En contraste, aunque las observaciones se realizaron durante más de diez años no se encontró evidencia de cambios temporales en la composición de especies. No obstante, algunas especies mostraron tendencias de aumento o disminución en su frecuencia. Presentamos el nuevo registro de una especie (Chloroceryle aenea) para la región. A pesar de que el paisaje asociado al río La Vieja ha sufrido un gran impacto antropogénico, aún conserva una diversidad significativa de aves acuáticas que pueden servir para aportar valor a los planes de conservación en la zona.

We compiled and analyzed data gathered from observations during the period 2001-2013 in three sectors along La Vieja river, located in the Cauca river valley, Colombia. We describe spatial and temporal aspects of such dataset, focusing in indentify patterns of species' composition and abundance. We recorded 28 waterbird species in 33 transects, being 22 species observed in more than 50 % of these transects. The species richness among transects did not shows significant differences. However, two cluster analyses, considering both presence/absence and abundance data, showed that there is spatial structure in the species composition along the river. In contrast, although observations were conducted during more than ten years there is no evidence of temporal changes in species composition. Still, some species showed increase or decrease trends in their frequency. We present a new record for one species (Chloroceryle aenea) for the region. Despite that the landscape surrounding La Vieja river have faced a high anthropogenic impact, the river still presents a significant diversity of waterbirds, which could add value to the conservation plans in the zone.

Multilocus analysis of intraspecific differentiation in three endemic bird species from the northern Neotropical dry forest.

Among-species phylogeographic concordance provides insight into the common processes driving lineage divergence in a particular region. However, identifying the processes that caused phylogeographic breaks is not always straight forward, and inferring past environmental conditions in combination with documented geologic events is sometimes necessary to explain current patterns. We searched for concordant phylogeographic patterns and investigated their causes in three bird species (Momotus mexicanus, Melanerpes chrysogenys, and Passerina leclancherii) that belong to three different avian orders and are endemic to the northernmost range of the Neotropical dry forest. We obtained mitochondrial DNA (ND2 and COI or cyt b) and nuclear DNA (20454, GAPDH, MUSK, and TGFB) sequences for at least one locus from 162 individuals across all species and defined climatically stable areas using environmental niche model projections for the last 130,000 years to have a paleoenvironmental framework for the phylogeographic results. All three species showed marked phylogeographic structure, with breaks found in roughly similar areas, such as the border between the Mexican states of Guerrero and Oaxaca, and between southern Jalisco and Michoacán. Both of these regions are known biogeographic breaks among other taxa. Patterns of genetic diversity and differentiation were partially compatible with climatically stable areas. Coalescent analyses revealed recent population growth and estimated the deeper haplogroup divergence of all three taxa to have occurred within the last 600,000 years. The phylogeographic patterns found are noteworthy because they are maintained in a relatively small area for bird species with continuous ranges, and highlight a unique situation when compared to phylogeographic patterns found in other studies of Neotropical birds that have stressed the role of geographic barriers to explain intraspecific differentiation. Our results point to a scenario of population isolation resulting in the present phylogeographic structure, likely a result of historical climate fluctuations that have fragmented and reconnected the Neotropical dry forest. This study contributes to a growing body of evidence indicating active diversification of endemic lineages in the northern Neotropical dry forest region.

The PREDICTS database: a global database of how local terrestrial biodiversity responds to human impacts.

Biodiversity continues to decline in the face of increasing anthropogenic pressures such as habitat destruction, exploitation, pollution and introduction of alien species. Existing global databases of species' threat status or population time series are dominated by charismatic species. The collation of datasets with broad taxonomic and biogeographic extents, and that support computation of a range of biodiversity indicators, is necessary to enable better understanding of historical declines and to project - and avert - future declines. We describe and assess a new database of more than 1.6 million samples from 78 countries representing over 28,000 species, collated from existing spatial comparisons of local-scale biodiversity exposed to different intensities and types of anthropogenic pressures, from terrestrial sites around the world. The database contains measurements taken in 208 (of 814) ecoregions, 13 (of 14) biomes, 25 (of 35) biodiversity hotspots and 16 (of 17) megadiverse countries. The database contains more than 1% of the total number of all species described, and more than 1% of the described species within many taxonomic groups - including flowering plants, gymnosperms, birds, mammals, reptiles, amphibians, beetles, lepidopterans and hymenopterans. The dataset, which is still being added to, is therefore already considerably larger and more representative than those used by previous quantitative models of biodiversity trends and responses. The database is being assembled as part of the PREDICTS project (Projecting Responses of Ecological Diversity In Changing Terrestrial Systems - http://www.predicts.org.uk). We make site-level summary data available alongside this article. The full database will be publicly available in 2015.

Molecular evidence of the taxonomic status of western Mexican populations of Pliaethornis longirostris (Aves: Trochilidae).

Species diversity is largely underestimated by current taxonomy, precluding a precise understanding of evolutionary processes. Genetic data have increased our understanding of that cryptic diversity, and multilocus studies are now desirable. In this study, we used mitochondrial and nuclear DNA sequences to evaluate the taxonomic status of the western Mexico's populations of Phaethornis longirostris. We found differences of 4.2 % in mtDNA and different alleles for one nDNA locus between western and eastern Mexican populations. Molecular and morphological evidence support the separation of these populations (P. 1. mexicanus and P. 1. griseoventer) as the species Phaethornis mexicanus Hartert 1897. Phaethornis mexicanus is endemic to western Mexico and sister to the remaining populations of P. longirostris. The speciation of P mexicanus probably occurred around 880,000 years ago by a vicariant event involving climatic-vegetational changes.

Filogeografía cmmparada: conceptos, métodos y patrones generales en aves neotropicaess / Comparative Phylogeography: Concepts, Methods and General Patterns in Neotropical Birds

Entender los patrones y procesos de diversificación de linajes intraespecíficos en el tiempo y en el espacio es el objetivo de la filogeografía. La comparación de estos patrones filogeográficos entre especies co-distribuidas muestra indicios de la historia de una comunidad. Aquí, reviso los conceptos y la metodología de la filogeografía comparada, un campo muy activo pero con métodos de análisis heterogéneos. Para dar un marco de referencia de la filogeografía en el Neotrópico, comento los patrones filogeográficos generales de las aves de esta región. La revisión de más de 100 estudios realizados en los últimos 25 años indica que los patrones filogeográficos de cada especie a pesar de coincidir en ciertos puntos con el de otras especies co-distribuidas tienen aspectos idiosincrásicos que indican que su historia es única.

Understanding the patterns and processes involved in intraspecific lineages diversification in time and space is the aim of phylogeography. The comparison of those phylogeographic patterns among co-distributed species shows insights of a community history. Here I review the concepts and methodologies of comparative phylogeography, an active research field that has heterogeneous analytical methods. In order to present a framework for phylogeography in the Neotropics, I comment the general phylogeographic patterns of the birds from this region. This review is based on more than 100 studies conducted during the last 25 years and indicate that despite different co-distributed species seem to share some points in their phylogeographic pattern they have idiosyncratic aspects, indicating an unique history for each one.

The differential effect of lowlands on the phylogeographic pattern of a Mesoamerican montane species (Lepidocolaptes affinis, Aves: Furnariidae).

We sequenced 1869 bp of mtDNA (cyt b and ND2) from 80 specimens of Lepidocolaptes affinis, a montane bird species of Mesoamerica, sampled at 34 localities from Mexico to Costa Rica. The species showed moderate genetic diversity (π=0.0045) and phylogeographic structure (Φ(ST)=0.12-0.95). The phylogeographic pattern indicated the Nicaragua Depression has prevented gene flow whereas populations on the two sides of the Isthmus of Tehuantepec did not show strong genetic differentiation. In Mexico, the population of the Sierra Madre Oriental was composed of two different lineages. In general, our data did not support a scenario of historical demographic expansion, and matched partially the phylogeographic patterns of other Mesoamerica montane species.