DOI: 10.5061/dryad.0k6djhb6x
title: Habitat simplification affects functional group structure along with taxonomic and phylogenetic diversity of temperate-zone ant assemblages over a ten-year period

description: Biodiversity is declining at various scales due to habitat simplification.
 Nevertheless, there is scarce information on how the biotic and abiotic
 changes linked to simplification affect several diversity dimensions, such
 as taxonomic, functional, and phylogenetic diversities. This study
 investigated whether transforming natural oak forests into induced
 grasslands affected species diversity, functional group structure, and
 phylogenetic diversity of ant assemblages inhabiting a temperate forest in
 central Mexico. We placed over 1,000 pitfall traps in five sampling events
 covering a ten-year period. We used Hill numbers to evaluate species
 diversity differences between vegetation types and patterns over time. Ant
 species were classified into stress-related functional groups, which were
 analyzed for their association with vegetation types and changes to their
 proportional abundance over time. We calculated the standardized effect
 size of the mean nearest taxon distance to quantify the evolutionary
 history and test for non-random patterns within vegetation types and
 sampling years. Species richness did not differ between vegetation types,
 yet grasslands showed greater diversity for the q=1 and q=2 orders.
 Besides, we found three ant species as bioindicators for each vegetation.
 Regarding functional structure, cold climate specialists were associated
 with oak forests. In contrast, generalist species were predominant in
 induced grasslands. Higher phylogenetic diversity with an overdispersed
 structure was associated with oak forest, whereas lower phylogenetic
 diversity and a clustered pattern were found in induced grassland. These
 results indicate that habitat simplification may not affect the number of
 ant species but rather increases their relative abundance and reorganizes
 the functional and phylogenetic structure in the ecosystem, particularly
 shift towards the dominance of evolutionary close-related species and
 broad-stress tolerant groups. These results highlight the importance of
 integrating further dimensions of diversity to properly evaluate the
 reassembly dynamics after habitat simplification and understand the
 mechanisms driving this biodiversity loss.
description: <strong>Study site</strong> The
 study was conducted in the temperate natural protected area of Flor del
 Bosque State Park (FBSP). The FBSP consists of 699.2 ha and is located in
 Puebla, Mexico (19°01'N, 98° 20'W, 2,225–2,400 m.a.s.l.). The
 climate is temperate-subhumid with an annual average temperature of 14 to
 16 °C and average annual precipitation of 750 to 950 mm. The rainy season
 occurs during the summer, and the dry season from November to April. The
 soil type is mainly lithosol and cambisol (Costes-Quijano et al., 2006).
 Its vegetation is composed of oak forest (41.71% of the park's
 surface), secondarily induced grassland (16.25%), and abandoned eucalyptus
 plantations (1.52%); the remaining 40.52% of the surface consists of
 thorny scrub and urban areas (Costes Quijano et al., 2006).
 <strong>Ant sampling</strong> Ant
 sampling was conducted in FBSP at six sampling events during the dry and
 rainy seasons, covering ten years. The sampling years were 2007, 2009,
 2015, 2016, and 2017 (Table 1). Oak forests and induced grasslands were
 included in each sampling event. Pitfall traps were placed in transects.
 S1 shows the coordinates of transects used in this study. The number of
 transects, pitfall traps, and distances between them varied depending on
 the year, but samplings generally kept the same basic characteristics
 (type of trap, vegetation type, season, Table 1). At each site, 10-20
 pitfall traps were placed per transect (spaced 5-20 m apart). Pitfall
 traps remained in the ground for 48-96 h. In total, data was obtained from
 1,080 pitfalls during the ten-year period. Ants collected from pitfall
 traps were stored in 70% ethanol and taken to the laboratory for
 identification. Ants were identified to the genus level using taxonomic
 keys. Specimens were sent to the following specialists for their
 identification: L. Quiroz, J. E. Valenzuela, G. R. Pérez-Toledo (Instituto
 de Ecología, A.C.), and W. Mackay (the University of Texas, Laboratory for
 Environmental Biology Centennial Museum). Ant specimens are kept in the
 UDLAP Formicidae and IEXA collections. The Secretaría de Medio Ambiente y
 Recursos Naturales (SEMARNAT) (Bureau of Environment and Natural
 Resources) approved the collection permit for this study
 SGPA/DGV/06901/15. Costes-Quijano, R., Meza, A. R.,
 Macías-Juárez, A., Berriel-Mastreta, C. A., Cortés-Atílano, B.,
 Martínez-Romero, L. E., & Hernández-Bautista, R. (2006). Plan de
 manejo parque ecológico recreativo General Lázaro Cárdenas Flor del
 Bosque. <em>Secretaría de Medio Ambiente y Recursos Naturales.
 Gobierno Del Estado de Puebla, Puebla</em>.
description: # Habitat simplification affects functional group structure along with
 taxonomic and phylogenetic diversity of temperate-zone ant assemblages
 over a ten-year period. ##
 Description of the data and file structure Data from S6 to S9 were
 utilized to compare alpha, functional, and phylogenetic diversity between
 a native oak forest and an induced grassland in a temperate forest in
 central Mexico **Authors** **Pérez-Toledo, G.** Red de Ecología Funcional,
 Instituto de Ecología AC, Carretera Antigua a Coatepec No. 351, El Haya,
 Xalapa, Veracruz 91070, México. **Cuautle,
 M.** Centro de Investigación en Ciencias Biológicas, Universidad Autónoma
 de Tlaxcala, Km 10.5 Autopista Tlaxcala-San Martín Texmelucan, San Felipe
 Ixtacuixtla, Tlaxcala 90120, México. 
 **Castillo-Guevara, C.** Centro de Investigación en Ciencias Biológicas,
 Universidad Autónoma de Tlaxcala, Km 10.5 Autopista Tlaxcala-San Martín
 Texmelucan, San Felipe Ixtacuixtla, Tlaxcala 90120, México.
 **Miguelena, J.G.** Arkansas State
 University, Campus Querétaro, Carrera Estatal 100, km 17.5. 76270. Colón,
 Querétaro, México. **File List** Table 1
 S1 Sampling_characteristics S3 Taxonomic_list_of_ant_species S6
 Taxonomic_matrix_ambient S7 Taxonomic_matrix_ambient_year S8
 Functional_groups S9 Functional groups_by_year TreesFB_100 **File
 descriptions** Table 1 Sampling characteristics (Type of trap, vegetation
 type, collecting liquid, pitfall size (cm), period of time (hrs), number
 of transects/vegetation/season, number of pitfall/transects, distance
 between pitfalls/year (m), sampling dates (day/month) for the different
 years in the study zone FBSP (Flor del Bosque State Park) S1 Year,
 vegetation type, season, transect code (TX = Transect number x), and
 geographic coordinates for the different points sampled in the study zone
 PSFB (Flor del Bosque State Park). S3 contains the taxonomic list of the
 ant species found, along with their frequencies (the number of times a
 particular ant species was found in a pitfall trap) in each vegetation
 type (Oak Forest and Induced Grassland) and sampling year (2007, 2009,
 2015, 2016, and 2017). S6 was employed to assess the alpha taxonomic
 diversity at order levels 0 (q=0), 1 (q=1), and 2 (q=2) (q=diversity
 order), for two vegetation types (Oak Forest and Induced Grassland),
 whereas S7 was utilized for the same assessment across multiple sampling
 years (2007, 2009, 2015, 2016, and 2017) within the same vegetation types.
 The databases contain frequencies for each ant species, indicating the
 number of times a particular ant species was found in a pitfall trap
 within each vegetation type and year. S8 was employed to compare
 proportions of functional groups for two vegetation types (Oak Forest and
 Induced grassland), while S9 was used for the same comparison across
 multiple sampling years (2007, 2009, 2015, 2016, and 2017). We implemented
 a proportion test based on a z-test of two proportions to assess whether
 functional groups were significantly associated with vegetation types. The
 "rstatix" package (Kassambara, 2020) was used for these
 analyses. The databases contain frequencies for each ant functional group,
 indicating the number of times a particular ant species within a specific
 functional group was found in a pitfall trap within each vegetation type
 and year. Functional group (FG) abbreviation stands for CCS: Cold Climate
 Specialists; GM: Generalist Myrmicinae; OP: Opportunists; SP: Specialist
 Predators; CS: Cryptic Species; HCS: Hot Climate Specialists; SC:
 Subordinate Camponotini. tressFB_100 Based on the most-recent backbone
 tree derived from a time-calibrated, genus-level phylogeny of Blanhard and
 Moreau, 2017, we simulated 100 species-level phylogenies using the list of
 ant species collected in the study area. The relationships within genera
 were obtained from a Yule (pure-birth) process using the
 *genus.to.species.tree* function in the "phytools" package
 (Revell, 2012). This data base contains the 100 phylogenies. Kassambara,
 A. (2020). rstatix: Pipe-friendly framework for basic statistical tests.
 In *R package version 0.6. 0*.
 Revell, L. J. (2012).
 phytools: an R package for phylogenetic comparative biology (and other
 things). *Methods in Ecology and Evolution*, *3*(2), 217–223.